Hi there Greg, I'm gonna take a stab at your post so bare with me LOL.
"Is it possible to have a trojan or virus installed in the BIOS"
Yes I believe it is possible but very rare anymore.
"Why was there 8 mb of space left."
I'm not positive on this one but it is normal and not a problem. It may be used to install the command console (which takes seven megs) to recover 2003.
I don't believe it would be possible to store a virus here, since there is no filesystem.
If you are still worried about this part of the disk I recommend a program called Driverscrubber (www.iolo.com). It will let you do a end-to-end wipe on the drive. Every sector on a disk is cleaned this way, first to last.
"For instance names of files the color changes to blue when before it was black,"
If a filename turn blue it means that the file has been compressed. This isn't a problem either. Windows compresses files that haven't been used in a certain amount of time.
"the system shuts down by itself."
This almost always means there is a hardware problem. This is where I believe your problem lies.
It could be something like bad ram, dirty case/overheating, improperly seated card or cable, crappy driver, weak or bad power supply or a number of other things.
This is what I would try,
1. Update all drivers.
2. Clean the inside of the case. Check all fans.
3. Reseat all cards/cables/ram.
4. Run a memory check (www.memtest86.com)
5. Run chkdsk on the your drive.
6. If your overclocking STOP until your problem if fixed.
If that doesn't work it may be time to start pulling out unnecessary cards to see what is casuing the problem.
Hope this helps,
Sandman