A few things pop to mind here.

Although remote, you may have a memory module going bad. Had to say that before
heading into the possible HD problem path.

The first reformat may have exposed a defect on the hard drive. A diagnostic tool
from the manufacture should be available to test the HD itself.

With all of the hardware pulling and changing, an IDE cable may have come loose.
Pulling a resetting the cables would be a good check of this. And on this line, was
the HD on the IDE cable by itself? Or did you remove a device. If you did remove a
device, did you verify that the remain HD didn't need a jumper reset to be
standalone?

Did you change any BIOS settings? Some of those can cause strange things to occur.

Are you overclocking? No judgment here, but MS OS installation programs have a track
record of being finicky in overclocked systems. Maybe setting the clock to normal to
do the install, then return to the overclocked state.

I think we would need more info to get much further...