Interesting that Spybot caught a trojan and AVG didn't, but the next step is to test for system stability. Did removing the trojan restore your access to your files by any chance? Have you lost critical files that you want to recover before we proceed with a Windows repair?

When was your last backup?

Anyway, assuming you're still missing a chunk of files I'd install an undelete application and try to recover any mission critical files. Not Windows files, you can't usually undelete them functionally, files that are personally important. Recover what you can and then back up all of the data you want to keep. Since we don't know how broken Windows might be I wouldn't make any assumptions about being able to preserve the data on the drive during the recovery process.

Here's an undelete application I've used:

http://undelete-plus.com/