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best suggestion i can give you is to get a copy of erd commander and put the registry back the way it was through that. erd commander may require you to have your raid driver floppy on hand to boot the erd commander environment, but otherwise it should be a piece of cake.
erd commander is a utility put out by winternals, a company specializing in windows NT bassed tools and utilities, and also known for having the free download "BSOD screensaver".
as far as i know windows determiones the C: drive by the master boot record. what it sounds like to me is that you had a raid array and at least one more hard drive in your system, and the hard drive was plugged into either the primary or secondary ide channel on the board. windows lables your hard drives in order starting from the primary master, then works its way through the drives present ont he secondary channel, then all subsequent devices (pci ide controllers, scsi controllers, etc). even if you choose to install windows on a drive other than the primary master, windows will always put the master boot record on the "first" hard drive (primary master, or, for example, the secondary slave if there is no hard drive on the primary channel at all nor on the secondary master).
the way i get around this problem is to unplug all my hard drives except the ones i am installing windows to (the raid array). after everything is done installing i can go back and plug everything in with no problems.
you may try copying all the hidden boot files over to the raid array from the current C: drive after you get your system to boot again, and then unplug your current C: drive and boot from the windows cd into the recovery console and run the "fixboot" command. this may re-write your boot sector so that your system boots from the raid array, and then you won't have to re-install.
after all is said and done, fixing the registry, and getting into the recovery console, you may find that it is faster to just go ahead and reinstall, so figure that out for yourself and you should have a good idea what you need to do next.
good luck!
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