The windows install is pre-chipset drivers. Is this an original MS Windows disc or a copy? Maybe try another disc?

The optical drive can be funky, but since the bootup from the HD taken so long...

I would reseat all the memory, cards and cables to ensure that they are seated properly. I would also check your BIOS to make sure the drive is detected properly and showing the correct speed (since you never mentioned if the drive was sata or pata).

I would probably change the CMOS battery (big silver button battery) and reset the BIOS also maybe flash the bios to a newer version if available. I would then reset to default and custom it.