Computer help?

Um, I've been having some problems with a corrupt registry. Some of y'all on my friends list are pretty good with this stuff, so I'd like your advice. I'm running Win2K.

Here's what happened:

I had reason to believe my power supply fan had just died. I overreacted and shut off the power supply switch, because I didn't want the death of my ps to damage any components.

After replacing the ps, I tried to start the computer, but no dice. It told me my winnt\system32\config\SYSTEMced was corrupt.

I unhooked drive 0 of my RAID array and tried booting from drive 1. Drive 1 got farther, but then got a blue screen that said that winnt\system32\config\software was corrupt, and that none of the backups or logs could be loaded.

I booted from the Win2K disk, went into the recovery console, replaced winnt\system32\config\system on drive 0 with the one from drive 1. It booted farther than it had before, but crapped out at the same place drive 1 did, on the "software" file.

I booted knoppix, and searched the internet for a while, finally deciding to do the Microsoft support page's suggestion to back up \config\system, software, sam, security, and default, then replace them with their backups from winnt\repair\. This worked... sort of. These backups were from January. No problem, I thought, I have a complete registry backup from much more recently than that.

Sadly, though, no matter what I do, I can't seem to replace/load/merge/whatever this .reg file with my current one, with regedit or regedt32 in regular or safe mode.

So I did what someone advised me not to: went back to the old version of system, sam, security, and default, but not software. It worked like a charm.

However, "software" (is this from HKEY_CURRENT_USER or HKEY_LOCAL_MACHINE?) is pretty darn important for, well, all my software. It's not just a matter of rebuilding my start menu. Some of my programs, especially stuff with copy protection registry keys, just doesn't work and will have to be reinstalled.

So, my questions are:

1) Is there any way to fix this?

2) How the hell am I really supposed to back up the registry in the future?

3) While I'm at it, is there a registry repair utility out there or any way within Windows to prune down my bloated registry? There was the REGEDIT /c thing for Win95. Is there something like this for Win2K? My registry is over 50 MB, so this is getting serious.