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One problem I've seen is the HDD cable going south (particularly new systems, or systems that have had the hard drive swapped out...) This can cause all kinds of flakey errors. Also, the controller can fail (drive controller), pretty rare, but still a posibility. We do hosting in our "other" life, and those two fall right behind a failed hard drive in these types of situations.
If you've replaced the hard drive, toss the cable, I never reuse them, particularly the 80 pin ATA 66+ cables. Maybe it's just me, but my data is worth more then the $5 the cable costs... :D
What makes me wonder is that the CD-Rom is showing a failure. The IDE controller on the master drive can cause issues, but it usually either works or doesn't.
Just some random thoughts on the problem.
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