I thought i would give it a shot just one more time with a few more troubleshooting steps:
I tried again with the HDD in, no boot, just got a happy face.
I tried using a floppy, no boot, just got a happy face.
Tried using a bootable CD ROM, again, the happy face.
In my last attempt, I made a bootable USB Key, and don't ask why, but it booted from the USB key and i was able to run the flash program.
I've put the computer back together and everything is working great. I'm running another Virus Scan just in case.