I would be inclined to re-install Windows from CD-ROM onto your hard disk drive. Also make sure that the hard disk drive you are using has its jumpers set to make it the master drive and that the IDE cable that links it to the motherboard is plugged into the primary IDE socket on the motherboard. If it's sharing the same IDE cable as the CD-ROM drive I would use a cable for each. Primary IDE to the HDD and the secondary IDE feeding the CD-ROM.
If all else fails do you have a spare HDD that you could use to rule out problems with the HDD you're trying to use.
I doesn't sound like you're too far from having a working computer there. If I think of anything else....
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