Thanks - I did run regedit and got rid of a bunch of stray SH3/Ubi references, and that seemed to work as far as getting the next install attempt to at least ask me for my CD key again.
Unfortunately, however, I'm still getting the reboot problem upon starting SH3 - it happens the same way every time - goes through the disk-checking routine, screen goes black, then monitor power/indicator light turns orange and the PC reboots. This happens when starting just SH3 1.0, as well as after patching to 1.4b - I haven't even bothered to try re-installing Sh3 Commander or GWX the last few times, since I can't get plain SH3 to work yet, so neither of them appear to be implicated at this point.
I have run virus/spyware checks, but no luck so far. I defragmented overnight, so I'm about to try it again. If that doesn't work, I guess I'll try to find a system restore point before this started happening and try that - if that fails I guess I'm looking at formatting and starting all over again with Windows
