Deleted corrupted files from Time Machine Backup

I have a 20" iMac that I've had since October 2008 and had no problems until now. My mac froze and I turned it off and I got the blue screen of death with a cursor meaning something was wrong. I contacted Apple Care and I was told to verify and repair permissions and the disk. I then waited 30mins and the computer got to a login screen and I was able to backup. The computer was taking 5 mins to do simple tasks. I was told to reinstall Snow Leopard and I did. That did not work and I ended up taking it to the Genius Bar where they couldn't fix the problem and said my HDD has failed and they replaced it with a new and bigger HDD . I then installed again on the new HDD and no problems. I got to the migration assistant where I then restored from a Time Machine backup. At the very end the migration freezes at "configuring network settings" or something like that. I turned off the machine and I got the blue screen of death forcing me to format the HDD and install again. I have now come to a conclusion part of the backup is corrupt somewhere in the operating system files. All I need is my personal user data. What folders should I delete? I already checked the backup and my personal files are fine.