Whoops! Moving Drupal installation directories... Help! .htaccess rebuild?

Well, I feel like an idiot.

This is my first drupal installation, and things have gone really well, I'm thrilled.
I installed drupal using simplescripts on my shared hosting environment. May not be classy, but it worked nicely.

I installed it into a /drupal folder, thinking I would just mess around with the thing. But then I themed it, installed ubercart, and customized all sorts of little details, and man! It was ready to go live!

So I read a bunch of posts about moving things, and it seemed pretty straightforward. I downloaded my whole drupal folder as a backup (via ftp... not the way to go i think) and then I moved all the files to the root directory and everything seemed to be working perfectly (again via ftp).

I deleted my old drupal folder. Which i think was a mistake.

Now, everything works fine as an unauthenticated user. But randomly, and inconsistantly, but maybe 50% of the time, links i click on within my store go to mydomain.com/drupal?=node/... instaid of mydomain.com/?=node/...

and I get a fat 404 Not Found. This happens at very inconvenient times.

Things i've tried:

1) Uncommented the $base_url from the settings.php file and set it to http://www.mydomain.com
2) cCeared my cache in the performance page. However, clicking the button sends me to a 404. I'm not sure if that's on the redirect back to the page, or during executing the actual command.... so I don't know if its working or not.
3) RewriteBase / added to my (very sparse) .htaccess file.

Now after reading more, I found out that I was supposed to use my cpanel file manager to move the files, and merge the .htaccess files. Since that file was invisible i dont think its around any more and didn't get downloaded or moved. DAMN!

Everything else seems to be fine, but its a massively irritating problem.
I've heard that i'm supposed to go into phpmyadmin and empty (not drop) all the tables that say "cache" in their name. Honestly that scares me. But if someone tells me it will fix the problem, i'll do it.

The problem i'm having goes something like this.

click a link > 404 error.
click back
click the link again >404 error.
click back
click the link again > works perfectly
click back
click the link again >404 error.

That's a little crazy for me...

What do i do!?

Right now my .htaccess file looks like this:

# Use PHP5 Single php.ini as default
AddHandler application/x-httpd-php5s .php

RewriteBase /  

I'd imagine there's supposed to be more in there than that but i have no idea what...

Thank you all for your help, I'm sorry if this is posted somewhere and I just cant put it all together.
Be well
-Avery