all if this started when i flashed the bios a couple months ago and totally incapacitated the machine, which could only be recovered by doing a crazy hotflash of the bios back to old version.
so i'm very hesitant to muck around with things too much more.
-mouser
Hotflashing - I bet that was fun

If it were me, (and based on the new info of having been hotflashed), test after each step stopping when/if it works:
1) First try the obvious as Carol has said, total reset of the BIOS settings. I'd add going into it on first boot and reset to Safe Defaults to see if the clock fires up.
2) Reflash the BIOS from
DOS - boot from a DOS 6/7 floppy or flash drive and do it the old fashioned way from the CLI. Just a mention here, you really should always flash the BIOS from DOS - there's just too many things going on in Windows to consider flashing reliably.
3) Remove the BIOS chip and then carefully reseat it back in again - this will wipe the contacts/pins and might clean up any suspect connection between the two - maybe it's not fully seated from it's previous removal.
4) If you had the equipment, (not many people do), I'd also consider removing the BIOS chip and programming using an (E)PROM/Flash programmer.
What was the motherboard?