upgrading site penalized me?

did i break the ranks?

[jake66]

i have redone my website from plain old html to a dynamic website run from php and myqsql. to be search engine friendly, i use mod_rewrite to make the urls like mysite.com/cat/bla+bla.html instead of mysite.com/index.php?=bla+bla

most of my hits came from google, an approx. 2-3 weeks ago they rid my site of all my best keywords.
now most of my hits are from msn, NONE from yahoo or any other search engine.

sure, my site is still IN google... but what good is it to anybody if they can't find me? don't they normally drop your result ranking before they eventually weed you out? what could have gotten my site a bad mark?

i never lost PR, but i lost my site in the results.
what used to be common keywords (for YEARS) people used to find my site, no longer exist.
i did htaccess 301's to nearly every item/category, they stayed there for a week or two after the site went up, but no longer exist

what else do i have to do to get myself back in the results? it's been up for over a month now. the PR came back, but the visitors didn't. day by day i seem to be getting less hits.

i have read on other sites using the meta nocache can penalize you... i had that on my secure/private pages only.
i used the noindex,nofollow on those pages as well.

i also had an affiliate program, which unbeknownst to me, is a bad thing?

i have removed all of the above, how long (on average) does it take for me to get back up to where i was?

also, when i look up link:www.mysite.com i do see a few pages (of my own url and people that link to me), some of them are (my site):
Title
Description
URL

others (my site):
Title only
does this hold significance to anything?