Trojan virus in latest iTunes download

I found some Trojan horse viruses in the latest iTunes version, and used the antivirus to clear out most of it. However, there was one Trojan left that the antivuris said was too big to archive (couldn't move it to the vault nor have the antivirus delete it), so I instead deleted the iTunes files containing the virus manually (including in the Recycle Bin), and now iTunes won't work. The file I downloaded was titled "iTunes1.8.6.4 internet cache" or something similar. When I try opening iTunes, I get an error message: something like "the file you are trying to download is on a network resource that is not available." I tried downloading iTunes again and setting it up, but get the same error message.

So my questions are,
1) How can I fix this problem? I'm guessing I need to download something to replace the files I lost, but where can I find safe copies of those since they don't seem to be the usual iTunes files?
2) How did a trojan horse appear only in iTunes files (roughly 100 or so) and nowhere else (did a virus scan of the whole computer -- nowhere else)? And how can I prevent this from happening again in the future?