These temp files can be deleted under Tools in Internet opions? (IE 6.0).

That will clean most of the files yes, but there are a couple that wont clean, you could clean them manually if you wanted, or you could try a program such as Ccleaner to do it all for you (www.ccleaner.com).

In the future, is it better to try to repair these files first and then move to chest or does it matter?

it depends on the malware, most malware these days can’t be cleaned as they are a ‘full program’ and infect your system rather then a specific file/folder. (someone else could will probably Describe this better for me I’m sure ;))

Why was Avast program sending a popup saying I was infected by these viruses if they caught them in time before they infected my computer?

These are programs/files that you receive from the internet web pages, and can initiate/work from these folders, so you are still infected if they are there.

–lee