Duplicate entry when updating (example is for Drupal 5 to Drupal 6 but could be use for others I guess)

We ran into the following failed attempts when trying to upgrade from drupal 5.7 to drupal 6.8:

Update #6043
Failed: ALTER TABLE {flood} ADD INDEX allow (event, hostname, timestamp) <-- index already exists?
Failed: ALTER TABLE {history} ADD INDEX nid (nid) <-- index already exists?
Failed: 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) <-- which part failed?
Failed: ALTER TABLE {blocks_roles} ADD INDEX rid (rid) <-- index exists?
Failed: ALTER TABLE {filters} DROP INDEX weight <-- index does NOT exist?
Failed: ALTER TABLE {filters} ADD UNIQUE KEY fmd (format, module, delta) <-- Are there filters we are not carrying forward with which we can drop data from?
Failed: ALTER TABLE {filters} ADD INDEX list (format, weight, module, delta) <-- index exists?
Failed: ALTER TABLE {node} DROP INDEX status <-- index does NOT exist?
Failed: ALTER TABLE {node} DROP KEY nid_vid <-- key does NOT exist?
Failed: ALTER TABLE {users} ADD INDEX mail <-- index already exists?
Failed: ALTER TABLE {users_roles} ADD INDEX rid (rid) <-- index already exists?
Failed: ALTER TABLE {contact} ADD INDEX list (weight, category) <-- index already exists?
Failed: ALTER TABLE {locales_target} ADD PRIMARY KEY (language, lid, plural) <-- does the locales_target table exist?
Failed: ALTER TABLE {profile_values} DROP INDEX uid <-- does the locales_target table exist?
Failed: ALTER TABLE {profile_values} ADD PRIMARY KEY (uid, fid)
Failed: ALTER TABLE {term_data} DROP INDEX vid
Failed: ALTER TABLE {term_data} ADD INDEX vid_name (vid, name)
Failed: ALTER TABLE {term_data} ADD INDEX taxonomy_tree (vid, weight, name)
Failed: ALTER TABLE {term_node} DROP PRIMARY KEY
Failed: ALTER TABLE {term_node} DROP INDEX tid
Failed: ALTER TABLE {term_node} ADD PRIMARY KEY (tid, vid)
Failed: ALTER TABLE {term_relation} DROP INDEX tid1
Failed: ALTER TABLE {term_relation} ADD UNIQUE KEY tid1_tid2 (tid1, tid2)
Failed: ALTER TABLE {term_synonym} DROP INDEX name
Failed: ALTER TABLE {term_synonym} ADD INDEX name_tid (name, tid)
Failed: ALTER TABLE {vocabulary} ADD INDEX list (weight, name)
Failed: ALTER TABLE {vocabulary_node_types} ADD INDEX vid (vid)

So we tried the suggested queries and here are the results we got:

SELECT format, module, delta, COUNT(*) FROM filters GROUP BY format, module, delta HAVING COUNT(*) > 1; - result - 0 rows
SELECT language, lid, plural, COUNT(*) FROM locales_target GROUP BY language, lid, plural HAVING COUNT(*) > 1; - result - unknown column language
SELECT nid, uid, hostname, COUNT(*) FROM poll_votes GROUP BY nid, uid, hostname HAVING COUNT(*) > 1; - result - poll_votes does not exist
SELECT uid, fid, COUNT(*) FROM profile_values GROUP BY uid, fid HAVING COUNT(*) > 1; - result - over 90,000 rows

I think select 2 and 3 results are because we didn't use a language module or the poll module in 5.7. I don't understand the result of the fourth select statement.

We tried the suggested remedy above but couldn't get it to work. I didn't see any other comments on this post to confirm if this is really a correct remedy.

From what we can tell a majority of the errors should be from duplicated keys but I think there maybe different reasons for some errors.

I know that we are not going from the latest version of drupal 5 but I read this thread and the poster tried upgrading to the latest version of drupal 5 and it had no effect:

http://drupal.org/node/357283

I am pretty sure we will be in the same boat. I can't believe how hard and tedious this drupal 5->6 upgrade is. I think a new version of drupal 6 needs to be released that better addresses these upgrade problems.

Some detailed upgrade advice would be greatly appreciated.

As soon as I:

ALTER IGNORE TABLE blocks ADD UNIQUE INDEX(theme, module, delta);

I get:

ERROR 1071 (42000): Specified key was too long; max key length is 1000 bytes

Any ideas? :-(