In addition to what Tim has suggested I'd try installing an OS to a 'bare-bones' machine.
I.e. RAM, CD-ROM and HD only. Remove all other hardware, PCI cards etc. etc. Have you anything unusual like a TV card or USB card ?
If you still have a problem it may be worth removing the RAM, stick by stick in case that's been upset - just to eliminate everything.
If you can get a stable OS running then reintroduce the hardware one component at a time.
My initial feeling is that it's very unlikely you have killed anything and that the Win2K registry possibly became corrupted. But then you've tried recovering the original OS and tried Win98 with a known good HD.
Good Luck