Unfortunately, if I understand your situation correctly, un-rooting isn't going to help you at this point. You need to replace the files you removed, and unless you know the exact names of the files on the filesystem (the app names will help you identify them, but they're not the same), it's an arduous process of trial and error. I'm going through it right now.
If you're not really confident with linux-esque stuff, reading and understanding log files, etc., my recommendation would be to use something (like Ti Backup Pro -- which is giving me hassles with two system apps, but generally does a good job of backup/restore with purchased/market apps) to backup all your apps & data that you might have customized, etc., then flash back to stock (there's some keypresses to do that, I don't remember them offhand), get the update, re-root, and re-install all your apps.
You'll need a few hours to do all that probably, but it CAN be done.