Files disappearing from 2nd hd

I have my bosses home computer I'm dealing with.
His symptoms were extremely long boot up(about 1 hr)
and near 100% cpu usage.
His son's routinely disabled the firewall and norton av software
to facilitate games and downloads.
He attempted to reinstall 2000, which did work. I ran trend micro
house call and detected 21 trojans, which I deleted.
The computer is a p3, running windows professional 2000.
There are 2 hds, a c 20 gb, and a d 120 gb. My recommendation
was to simply
remove the c drive, and replace it with a newer, much larger
drive, an 80 gb. I also recommended that he use xp pro.
I followed through, with the recommedation, and everything
seemed well. I also reinstalled his norton nav, ran through one
final scan, and everything went well. There were some adware
items in the D:Restore\TEMP directory(about 300) that norton
was unable to delete. All his other remaining files were still
there.
He took the machine home, attempted to install his isp apps
along with Limewire,and some others. He discovered that his
files were no longer on his D drive. He claimed to not have
erased them. I had him bring the machine back. I was able to
see some of the directories that were there when I had it, but
they are largely emptied.
At this point, I am at a complete loss as to how the files and
directories could have come up missing, short of some still
existing viral activity, or something with installing the new c drive
with a fresh os. Any tips or thoughts would be greatly
appreciated.
Don Hassler