Upgrade from 5.11 to 6.8

I just upgraded to Drupal 6 using Greggles video, but it didn't go as smoothly as his example did. The first reason for this is because apparently my host (or something on my end) has it so that if a folder is replaced, it deletes the contents before copying it over - meaning I lost all of my settings and modules. That's not a huge deal since I made a back up, but after running the update script I got the following errors at the top in red:

* user warning: Table 'cache_form' already exists query: CREATE TABLE cache_form ( cid varchar(255) NOT NULL default '', data longblob, expire int NOT NULL default '0', created int NOT NULL default '0', headers text, serialized int(1) NOT NULL default '0', PRIMARY KEY (cid), INDEX expire (expire) ) /*!40100 DEFAULT CHARACTER SET UTF8 */ in /home/foo/public_html/modules/system/system.install on line 1399.
* user warning: Table 'menu_router' already exists query: CREATE TABLE menu_router ( `path` VARCHAR(255) NOT NULL DEFAULT '', `load_functions` VARCHAR(255) NOT NULL DEFAULT '', `to_arg_functions` VARCHAR(255) NOT NULL DEFAULT '', `access_callback` VARCHAR(255) NOT NULL DEFAULT '', `access_arguments` TEXT DEFAULT NULL, `page_callback` VARCHAR(255) NOT NULL DEFAULT '', `page_arguments` TEXT DEFAULT NULL, `fit` INT NOT NULL DEFAULT 0, `number_parts` SMALLINT NOT NULL DEFAULT 0, `tab_parent` VARCHAR(255) NOT NULL DEFAULT '', `tab_root` VARCHAR(255) NOT NULL DEFAULT '', `title` VARCHAR(255) NOT NULL DEFAULT '', `title_callback` VARCHAR(255) NOT NULL DEFAULT '', `title_arguments` VARCHAR(255) NOT NULL DEFAULT '', `type` INT NOT NULL DEFAULT 0, `block_callback` VARCHAR(255) NOT NULL DEFAULT '', `description` TEXT NOT NULL, `position` VARCHAR(255) NOT NULL DEFAULT '', `weight` INT NOT NULL DEFAULT 0, `file` MEDIUMTEXT DEFAULT NULL, PRIMARY KEY (path), INDEX fit (fit), INDEX tab_parent (tab_parent) ) /*!40100 DEFAULT CHARACTER SET UTF8 */ in /home/foo/public_html/includes/database.inc on line 515.
* user warning: Table 'menu_links' already exists query: CREATE TABLE menu_links ( `menu_name` VARCHAR(32) NOT NULL DEFAULT '', `mlid` INT unsigned NOT NULL auto_increment, `plid` INT unsigned NOT NULL DEFAULT 0, `link_path` VARCHAR(255) NOT NULL DEFAULT '', `router_path` VARCHAR(255) NOT NULL DEFAULT '', `link_title` VARCHAR(255) NOT NULL DEFAULT '', `options` TEXT DEFAULT NULL, `module` VARCHAR(255) NOT NULL DEFAULT 'system', `hidden` SMALLINT NOT NULL DEFAULT 0, `external` SMALLINT NOT NULL DEFAULT 0, `has_children` SMALLINT NOT NULL DEFAULT 0, `expanded` SMALLINT NOT NULL DEFAULT 0, `weight` INT NOT NULL DEFAULT 0, `depth` SMALLINT NOT NULL DEFAULT 0, `customized` SMALLINT NOT NULL DEFAULT 0, `p1` INT unsigned NOT NULL DEFAULT 0, `p2` INT unsigned NOT NULL DEFAULT 0, `p3` INT unsigned NOT NULL DEFAULT 0, `p4` INT unsigned NOT NULL DEFAULT 0, `p5` INT unsigned NOT NULL DEFAULT 0, `p6` INT unsigned NOT NULL DEFAULT 0, `p7` INT unsigned NOT NULL DEFAULT 0, `p8` INT unsigned NOT NULL DEFAULT 0, `p9` INT unsigned NOT NULL DEFAULT 0, `updated` SMALLINT NOT NULL DEFAULT 0, PRIMARY KEY (mlid), INDEX path_menu (link_path(128), menu_name), INDEX menu_plid_expand_child (menu_name, plid, expanded, has_children), INDEX menu_parents (menu_name, p1, p2, p3, p4, p5, p6, p7, p8, p9), INDEX router_path (router_path(128)) ) /*!40100 DEFAULT CHARACTER SET UTF8 */ in /home/foo/public_html/includes/database.inc on line 515.
* user warning: Table 'actions_aid' already exists query: CREATE TABLE actions_aid ( `aid` INT unsigned NOT NULL auto_increment, PRIMARY KEY (aid) ) /*!40100 DEFAULT CHARACTER SET UTF8 */ in /home/foo/public_html/includes/database.inc on line 515.
* user warning: Duplicate entry '1-filter-1' for key 2 query: ALTER TABLE filters ADD UNIQUE KEY fmd (format, module, delta) in /home/foo/public_html/includes/database.mysql-common.inc on line 403.
---------------------------

And I looked down through the list of actions taken to update, and there were some failures. Here is that list:

---------------------------
The following queries were executed
system module
Update #6000

* ALTER TABLE {boxes} CHANGE COLUMN bid bid int NOT NULL
* REPLACE INTO {sequences} VALUES ('{boxes}_bid', 0)

Update #6001

* ALTER TABLE {term_node} ADD `vid` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {term_node} DROP PRIMARY KEY
* ALTER TABLE {term_node} ADD PRIMARY KEY (vid, tid, nid)
* ALTER TABLE {term_node} ADD INDEX vid (vid)

Update #6002

* ALTER TABLE {variable} DROP PRIMARY KEY
* ALTER TABLE {variable} CHANGE name `name` VARCHAR(128) NOT NULL DEFAULT ''
* ALTER TABLE {variable} ADD PRIMARY KEY (name)

Update #6003

* ALTER TABLE {comments} ADD INDEX status (status)

Update #6004

* No queries

Update #6005

* ALTER TABLE {url_alias} ADD language varchar(12) NOT NULL default ''
* ALTER TABLE {url_alias} DROP INDEX dst
* ALTER TABLE {url_alias} ADD UNIQUE dst_language (dst, language)

Update #6006

* ALTER TABLE {node_counter} DROP INDEX daycount
* ALTER TABLE {node_counter} DROP INDEX totalcount
* ALTER TABLE {node_counter} DROP INDEX timestamp

Update #6007

* UPDATE {watchdog} SET severity = 5 WHERE severity = 0
* UPDATE {watchdog} SET severity = 4 WHERE severity = 1
* UPDATE {watchdog} SET severity = 3 WHERE severity = 2

Update #6008

* UPDATE {system} SET owner = description
* ALTER TABLE {system} DROP description

Update #6009

* UPDATE {system} SET status = 1 WHERE name = 'php' AND type = 'module'
* UPDATE {filters} SET delta = 0, module = 'php' WHERE module = 'filter' AND delta = 1
* UPDATE {filters} SET delta = 1 WHERE module = 'filter' AND delta = 2
* UPDATE {filters} SET delta = 2 WHERE module = 'filter' AND delta = 3

Update #6010

* ALTER TABLE {watchdog} ADD `variables` LONGTEXT DEFAULT NULL
* UPDATE {watchdog} SET variables = '%s' (N;)
* ALTER TABLE {watchdog} CHANGE variables `variables` LONGTEXT NOT NULL

Update #6011

* ALTER TABLE {node} ADD language varchar(12) NOT NULL default ''

Update #6012

* No queries

Update #6013

* Cache rebuilt.

Update #6014

* variable_set('install_task')

Update #6015

* Failed: CREATE TABLE {cache_form} ( cid varchar(255) NOT NULL default '', data longblob, expire int NOT NULL default '0', created int NOT NULL default '0', headers text, serialized int(1) NOT NULL default '0', PRIMARY KEY (cid), INDEX expire (expire) ) /*!40100 DEFAULT CHARACTER SET UTF8 */

Update #6016

* ALTER TABLE {node} ADD UNIQUE KEY nid_vid (nid, vid)
* ALTER TABLE {blocks} ADD bid int NOT NULL AUTO_INCREMENT PRIMARY KEY
* ALTER TABLE {filters} ADD fid int NOT NULL AUTO_INCREMENT PRIMARY KEY
* ALTER TABLE {flood} ADD fid int NOT NULL AUTO_INCREMENT PRIMARY KEY
* ALTER TABLE {permission} ADD pid int NOT NULL AUTO_INCREMENT PRIMARY KEY
* ALTER TABLE {term_relation} ADD trid int NOT NULL AUTO_INCREMENT PRIMARY KEY
* ALTER TABLE {term_synonym} ADD tsid int NOT NULL AUTO_INCREMENT PRIMARY KEY

Update #6017

* variable_set(user_mail_register_admin_created_subject)
* variable_del(user_mail_admin_subject)
* variable_set(user_mail_register_admin_created_body)
* variable_del(user_mail_admin_body)
* variable_set(user_mail_register_pending_approval_subject)
* variable_del(user_mail_approval_subject)
* variable_set(user_mail_register_pending_approval_body)
* variable_del(user_mail_approval_body)
* variable_set(user_mail_register_no_approval_required_subject)
* variable_del(user_mail_welcome_subject)
* variable_set(user_mail_register_no_approval_required_body)
* variable_del(user_mail_welcome_body)
* variable_set(user_mail_password_reset_subject)
* variable_del(user_mail_pass_subject)
* variable_set(user_mail_password_reset_body)
* variable_del(user_mail_pass_body)

Update #6018

* HTML corrector filter added to the 'Filtered HTML' input format.
* HTML corrector filter added to the 'Full HTML' input format.

Update #6019

* ALTER TABLE {boxes} CHANGE format `format` SMALLINT NOT NULL DEFAULT 0
* ALTER TABLE {comments} CHANGE format `format` SMALLINT NOT NULL DEFAULT 0
* ALTER TABLE {comments} DROP INDEX lid
* ALTER TABLE {comments} ADD INDEX nid (nid)
* ALTER TABLE {cache} CHANGE serialized `serialized` SMALLINT NOT NULL DEFAULT 0
* ALTER TABLE {cache_filter} CHANGE serialized `serialized` SMALLINT NOT NULL DEFAULT 0
* ALTER TABLE {cache_page} CHANGE serialized `serialized` SMALLINT NOT NULL DEFAULT 0
* ALTER TABLE {cache_form} CHANGE serialized `serialized` SMALLINT NOT NULL DEFAULT 0
* UPDATE {users} SET uid = 49 WHERE uid = 0
* ALTER TABLE {users} DROP PRIMARY KEY
* ALTER TABLE {users} CHANGE uid `uid` INT unsigned NOT NULL auto_increment, ADD PRIMARY KEY (uid)
* UPDATE {users} SET uid = 0 WHERE uid = 49
* ALTER TABLE {boxes} DROP PRIMARY KEY
* ALTER TABLE {boxes} CHANGE bid `bid` INT unsigned NOT NULL auto_increment, ADD PRIMARY KEY (bid)
* ALTER TABLE {files} DROP PRIMARY KEY
* ALTER TABLE {files} CHANGE fid `fid` INT unsigned NOT NULL auto_increment, ADD PRIMARY KEY (fid)
* ALTER TABLE {node} DROP PRIMARY KEY
* ALTER TABLE {node} CHANGE nid `nid` INT unsigned NOT NULL auto_increment, ADD PRIMARY KEY (nid)
* ALTER TABLE {node_revisions} DROP PRIMARY KEY
* ALTER TABLE {node_revisions} CHANGE vid `vid` INT unsigned NOT NULL auto_increment, ADD PRIMARY KEY (vid)

Update #6020

* Failed: CREATE TABLE {menu_router} ( `path` VARCHAR(255) NOT NULL DEFAULT '', `load_functions` VARCHAR(255) NOT NULL DEFAULT '', `to_arg_functions` VARCHAR(255) NOT NULL DEFAULT '', `access_callback` VARCHAR(255) NOT NULL DEFAULT '', `access_arguments` TEXT DEFAULT NULL, `page_callback` VARCHAR(255) NOT NULL DEFAULT '', `page_arguments` TEXT DEFAULT NULL, `fit` INT NOT NULL DEFAULT 0, `number_parts` SMALLINT NOT NULL DEFAULT 0, `tab_parent` VARCHAR(255) NOT NULL DEFAULT '', `tab_root` VARCHAR(255) NOT NULL DEFAULT '', `title` VARCHAR(255) NOT NULL DEFAULT '', `title_callback` VARCHAR(255) NOT NULL DEFAULT '', `title_arguments` VARCHAR(255) NOT NULL DEFAULT '', `type` INT NOT NULL DEFAULT 0, `block_callback` VARCHAR(255) NOT NULL DEFAULT '', `description` TEXT NOT NULL, `position` VARCHAR(255) NOT NULL DEFAULT '', `weight` INT NOT NULL DEFAULT 0, `file` MEDIUMTEXT DEFAULT NULL, PRIMARY KEY (path), INDEX fit (fit), INDEX tab_parent (tab_parent) ) /*!40100 DEFAULT CHARACTER SET UTF8 */
* Failed: CREATE TABLE {menu_links} ( `menu_name` VARCHAR(32) NOT NULL DEFAULT '', `mlid` INT unsigned NOT NULL auto_increment, `plid` INT unsigned NOT NULL DEFAULT 0, `link_path` VARCHAR(255) NOT NULL DEFAULT '', `router_path` VARCHAR(255) NOT NULL DEFAULT '', `link_title` VARCHAR(255) NOT NULL DEFAULT '', `options` TEXT DEFAULT NULL, `module` VARCHAR(255) NOT NULL DEFAULT 'system', `hidden` SMALLINT NOT NULL DEFAULT 0, `external` SMALLINT NOT NULL DEFAULT 0, `has_children` SMALLINT NOT NULL DEFAULT 0, `expanded` SMALLINT NOT NULL DEFAULT 0, `weight` INT NOT NULL DEFAULT 0, `depth` SMALLINT NOT NULL DEFAULT 0, `customized` SMALLINT NOT NULL DEFAULT 0, `p1` INT unsigned NOT NULL DEFAULT 0, `p2` INT unsigned NOT NULL DEFAULT 0, `p3` INT unsigned NOT NULL DEFAULT 0, `p4` INT unsigned NOT NULL DEFAULT 0, `p5` INT unsigned NOT NULL DEFAULT 0, `p6` INT unsigned NOT NULL DEFAULT 0, `p7` INT unsigned NOT NULL DEFAULT 0, `p8` INT unsigned NOT NULL DEFAULT 0, `p9` INT unsigned NOT NULL DEFAULT 0, `updated` SMALLINT NOT NULL DEFAULT 0, PRIMARY KEY (mlid), INDEX path_menu (link_path(128), menu_name), INDEX menu_plid_expand_child (menu_name, plid, expanded, has_children), INDEX menu_parents (menu_name, p1, p2, p3, p4, p5, p6, p7, p8, p9), INDEX router_path (router_path(128)) ) /*!40100 DEFAULT CHARACTER SET UTF8 */

Update #6021

* ALTER TABLE {menu} ADD `converted` TINYINT unsigned NOT NULL DEFAULT 0
* CREATE TABLE {menu_custom} ( `menu_name` VARCHAR(32) NOT NULL DEFAULT '', `title` VARCHAR(255) NOT NULL DEFAULT '', `description` TEXT DEFAULT NULL, PRIMARY KEY (menu_name) ) /*!40100 DEFAULT CHARACTER SET UTF8 */
* UPDATE {menu_custom} SET menu_name = 'primary-links', description = 'Primary links are often used at the theme layer to show the major sections of a site. A typical representation for primary links would be tabs along the top.' WHERE menu_name = 'menu-primary-links'
* UPDATE {menu_links} SET menu_name = 'primary-links' WHERE menu_name = 'menu-primary-links'
* UPDATE {blocks} SET delta = 'primary-links' WHERE module = 'menu' AND delta = '2'
* UPDATE {blocks_roles} SET delta = 'primary-links' WHERE module = 'menu' AND delta = '2'
* UPDATE {blocks} SET delta = 'menu-members-only-me' WHERE module = 'menu' AND delta = '121'
* UPDATE {blocks_roles} SET delta = 'menu-members-only-me' WHERE module = 'menu' AND delta = '121'
* UPDATE {blocks} SET delta = 'menu-footermenu' WHERE module = 'menu' AND delta = '54'
* UPDATE {blocks_roles} SET delta = 'menu-footermenu' WHERE module = 'menu' AND delta = '54'
* UPDATE {blocks} SET delta = 'menu-add-content' WHERE module = 'menu' AND delta = '163'
* UPDATE {blocks_roles} SET delta = 'menu-add-content' WHERE module = 'menu' AND delta = '163'
* UPDATE {blocks} SET delta = 'menu-infolists' WHERE module = 'menu' AND delta = '169'
* UPDATE {blocks_roles} SET delta = 'menu-infolists' WHERE module = 'menu' AND delta = '169'
* UPDATE {blocks} SET delta = 'menu-alumni' WHERE module = 'menu' AND delta = '172'
* UPDATE {blocks_roles} SET delta = 'menu-alumni' WHERE module = 'menu' AND delta = '172'
* Relocated 168 existing items to the new menu system.
* DROP TABLE {menu}

Update #6022

* ALTER TABLE {files} DROP INDEX nid
* ALTER TABLE {files} CHANGE nid `uid` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {files} ADD `status` INT NOT NULL DEFAULT 0
* ALTER TABLE {files} ADD `timestamp` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {files} ADD INDEX uid (uid)
* ALTER TABLE {files} ADD INDEX status (status)
* ALTER TABLE {files} ADD INDEX timestamp (timestamp)
* ALTER TABLE {file_revisions} DROP PRIMARY KEY
* ALTER TABLE {file_revisions} DROP INDEX vid
* ALTER TABLE {file_revisions} RENAME TO {upload}
* ALTER TABLE {upload} ADD `nid` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {upload} ADD INDEX nid (nid)
* ALTER TABLE {upload} ADD PRIMARY KEY (vid, fid)
* ALTER TABLE {upload} ADD INDEX fid (fid)
* UPDATE {files} SET status = 1

Update #6023

* ALTER TABLE {node_revisions} DROP INDEX nid
* ALTER TABLE {node_revisions} CHANGE nid `nid` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {node_revisions} ADD INDEX nid (nid)

Update #6024

* ALTER TABLE {node} ADD `tnid` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {node} ADD `translate` INT NOT NULL DEFAULT 0
* ALTER TABLE {node} ADD INDEX tnid (tnid)
* ALTER TABLE {node} ADD INDEX translate (translate)

Update #6025

* ALTER TABLE {node} DROP INDEX node_title_type
* ALTER TABLE {node} CHANGE title `title` VARCHAR(255) NOT NULL DEFAULT ''
* ALTER TABLE {node} ADD INDEX node_title_type (title, type(4))
* ALTER TABLE {node_revisions} CHANGE title `title` VARCHAR(255) NOT NULL DEFAULT ''

Update #6026

* No queries

Update #6027

* ALTER TABLE {blocks} ADD `cache` TINYINT NOT NULL DEFAULT 1

Update #6028

* No queries

Update #6029

* 'dblog' module enabled.

Update #6030

* ALTER TABLE {actions} RENAME TO {actions_old_contrib}
* CREATE TABLE {actions} ( `aid` VARCHAR(255) NOT NULL DEFAULT '0', `type` VARCHAR(32) NOT NULL DEFAULT '', `callback` VARCHAR(255) NOT NULL DEFAULT '', `parameters` LONGTEXT NOT NULL, `description` VARCHAR(255) NOT NULL DEFAULT '0', PRIMARY KEY (aid) ) /*!40100 DEFAULT CHARACTER SET UTF8 */
* Failed: CREATE TABLE {actions_aid} ( `aid` INT unsigned NOT NULL auto_increment, PRIMARY KEY (aid) ) /*!40100 DEFAULT CHARACTER SET UTF8 */

Update #6031

* No queries

Update #6032

* ALTER TABLE {profile_fields} DROP KEY name
* ALTER TABLE {profile_fields} CHANGE name `name` VARCHAR(128) NOT NULL DEFAULT ''
* ALTER TABLE {profile_fields} ADD UNIQUE KEY name (name)

Update #6033

* ALTER TABLE {node_comment_statistics} CHANGE nid `nid` INT unsigned NOT NULL DEFAULT 0

Update #6034

* UPDATE {permission} SET perm = 'access administration menu, display drupal links, administer blocks, use PHP for block visibility, access chat rooms, administer chat rooms, administer chats, create chat rooms, create chats, edit own chat rooms, access comments, administer comments, post comments, post comments without approval, access site-wide contact form, administer filters, administer forums, create forum topics, edit own forum topics, create images, edit images, edit own images, view original images, administer images, import images, administer imagecache, flush imagecache, administer menu, access content, administer content types, administer nodes, create page content, create story content, edit own page content, edit own story content, edit page content, edit story content, revert revisions, view revisions, administer url aliases, create url aliases, cancel own vote, create polls, inspect all votes, vote on polls, access private content, edit private content, mark content as private, access administration pages, administer site configuration, select different theme, edit tables, administer taxonomy, administer catalog, view catalog, administer order workflow, create orders, delete any order, delete orders, edit orders, view all orders, delete payments, manual payments, view payments, administer paypal, administer product classes, administer product features, administer products, create products, edit own products, edit products, configure quotes, view reports, view all role expirations, administer store, view customers, view store reports, upload files, view uploaded files, access user profiles, administer permissions, administer users, change own username, access all views, administer views' WHERE rid = 3

Update #6035

* ALTER TABLE {system} DROP INDEX weight
* ALTER TABLE {system} ADD INDEX modules (type(12), status, weight, filename)
* ALTER TABLE {system} ADD INDEX bootstrap (type(12), status, bootstrap, weight, filename)

Update #6036

* No queries

Update #6037

* ALTER TABLE {blocks} CHANGE region `region` VARCHAR(64) NOT NULL DEFAULT ''
* UPDATE {blocks} SET region = '' WHERE status = 0

Update #6038

* UPDATE {profile_fields} SET category = 'Account settings' WHERE LOWER(category) = 'account'

Update #6039

* UPDATE {permission} SET perm = 'access chat rooms, access comments, post comments, post comments without approval, access site-wide contact form, create forum topics, edit own forum topics, create images, edit own images, view original images, access content, create bio content, edit own bio content, edit own earticle content, vote on polls, access private content, edit any private content, mark content as private, view catalog, access user profiles' WHERE rid = 2
* UPDATE {permission} SET perm = 'access administration menu, display drupal links, administer blocks, use PHP for block visibility, access chat rooms, administer chat rooms, administer chats, create chat rooms, create chats, edit own chat rooms, access comments, administer comments, post comments, post comments without approval, access site-wide contact form, administer filters, administer forums, create forum topics, edit own forum topics, create images, edit images, edit own images, view original images, administer images, import images, administer imagecache, flush imagecache, administer menu, access content, administer content types, administer nodes, create page content, create story content, edit own page content, edit own story content, edit any page content, edit any story content, revert revisions, view revisions, administer url aliases, create url aliases, cancel own vote, create poll content, inspect all votes, vote on polls, access private content, edit any private content, mark content as private, access administration pages, administer site configuration, select different theme, edit tables, administer taxonomy, administer catalog, view catalog, administer order workflow, create orders, delete any order, delete orders, edit orders, view all orders, delete payments, manual payments, view payments, administer paypal, administer product classes, administer product features, administer products, create products, edit own products, edit products, configure quotes, view reports, view all role expirations, administer store, view customers, view store reports, upload files, view uploaded files, access user profiles, administer permissions, administer users, change own username, access all views, administer views' WHERE rid = 3
* UPDATE {permission} SET perm = 'create minutes content, create pres_blog content, edit any minutes content, edit own minutes content, edit own pres_blog content, edit any pres_blog content' WHERE rid = 9

Update #6040

* ALTER TABLE {upload} ADD `weight` TINYINT NOT NULL DEFAULT 0

Update #6041

* UPDATE {vocabulary} SET required = 0 WHERE vid = 1
* UPDATE {system} SET weight = 1 WHERE name = 'forum'

Update #6042

* No queries

Update #6043

* ALTER TABLE {flood} ADD INDEX allow (event, hostname, timestamp)
* ALTER TABLE {history} ADD INDEX nid (nid)
* ALTER TABLE {blocks} CHANGE theme `theme` VARCHAR(64) NOT NULL DEFAULT '', ADD UNIQUE KEY tmd (theme, module, delta), ADD INDEX list (theme, status, region, weight, module)
* ALTER TABLE {blocks_roles} ADD INDEX rid (rid)
* ALTER TABLE {filters} DROP INDEX weight
* Failed: ALTER TABLE {filters} ADD UNIQUE KEY fmd (format, module, delta)
* ALTER TABLE {filters} ADD INDEX list (format, weight, module, delta)
* ALTER TABLE {node} DROP INDEX status
* ALTER TABLE {node} DROP KEY nid_vid
* ALTER TABLE {users} ADD INDEX mail (mail)
* ALTER TABLE {users_roles} ADD INDEX rid (rid)
* ALTER TABLE {contact} ADD INDEX list (weight, category)
* ALTER TABLE {poll_votes} DROP INDEX nid
* ALTER TABLE {poll_votes} ADD PRIMARY KEY (nid, uid, hostname)
* ALTER TABLE {profile_values} DROP INDEX uid
* ALTER TABLE {profile_values} DROP INDEX fid
* ALTER TABLE {profile_values} CHANGE fid `fid` INT unsigned NOT NULL DEFAULT 0, ADD INDEX fid (fid)
* ALTER TABLE {profile_values} CHANGE uid `uid` INT unsigned NOT NULL DEFAULT 0
* ALTER TABLE {profile_values} ADD PRIMARY KEY (uid, fid)
* ALTER TABLE {term_data} DROP INDEX vid
* ALTER TABLE {term_data} ADD INDEX vid_name (vid, name)
* ALTER TABLE {term_data} ADD INDEX taxonomy_tree (vid, weight, name)
* ALTER TABLE {term_node} DROP PRIMARY KEY
* ALTER TABLE {term_node} DROP INDEX tid
* ALTER TABLE {term_node} ADD PRIMARY KEY (tid, vid)
* ALTER TABLE {term_relation} DROP INDEX tid1
* ALTER TABLE {term_relation} ADD UNIQUE KEY tid1_tid2 (tid1, tid2)
* ALTER TABLE {term_synonym} DROP INDEX name
* ALTER TABLE {term_synonym} ADD INDEX name_tid (name, tid)
* ALTER TABLE {vocabulary} ADD INDEX list (weight, name)
* ALTER TABLE {vocabulary_node_types} DROP PRIMARY KEY
* ALTER TABLE {vocabulary_node_types} ADD PRIMARY KEY (type, vid)
* ALTER TABLE {vocabulary_node_types} ADD INDEX vid (vid)

Update #6044

* DELETE FROM {term_node} WHERE vid = 0

Update #6045

* No queries

Update #6046

* No queries

Update #6047

* UPDATE {blocks} SET cache = -1 WHERE module = 'user' AND delta IN ('0', '1')
* UPDATE {blocks} SET cache = -1 WHERE module = 'system' AND delta = '0'

Update #6048

* ALTER TABLE {menu_router} CHANGE load_functions `load_functions` TEXT NOT NULL
* ALTER TABLE {menu_router} CHANGE to_arg_functions `to_arg_functions` TEXT NOT NULL

comment module
Update #6001

* ALTER TABLE {comments} DROP score
* ALTER TABLE {comments} DROP users

Update #6002

* Global comment settings copied to all node types.

Update #6003

* ALTER TABLE {comments} ADD INDEX pid (pid)

forum module
Update #6000

* No queries
---------------------------

I wasn't sure what to do, so I continued and everything LOOKS ok. I'm not getting any weird errors (except that my chat rooms are missing). Everything looks fine. So my question is, should I be worried? Is this going to come back and bite me later?

Thanks in advance!