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The problem I see is that the Windows registry probably has hard coded paths to the files, so if your main HD in Windows was showing as D: even after you write a loader to the boot sector it may present itself as C: instead, which will totally screw up a lot of stuff in your registry.
At least, that is what happened to me last time I did that ... but it has been 18 years since I've really done anything with windows besides wipe a drive and reinstall from scratch ... so I would hope that in half a dozen releases and countless service packs that has been "fixed".
Anyway, you'll want a recovery/install disk, boot wtih it, tell it where to write the bootloader and you are good to go.
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