Somewhat curious .. but have you attempted re-running / re-installing Boot Camp?
(caveat emptor: I'm not a Windows person, even a little bit, so any advice offered is pure guesswork..)
Well I've never used Boot Camp before myself (let alone a Mac seriously), and so caveat emptor from me too, but from what you are proposing I would've thought all that would do is write a new partition with new MFT and thus it is "just as new" (keeping in mind that data is never really "erased", it just gets overwritten, unless you do something exceptional).
If Boot Camp were smart enough to pick up the partition and, say, simply repair the boot record or the like, then there really should be no problem for our OP to take care of that by himself, even without having to have Boot Camp do the job. From what the OP is describing, the essential file system data might be corrupted.
I have doubts that given the ineptitude of Apple in this respect that they would be ironically skilled enough to pick up pieces of a file system and somehow reconstruct / resurrect the former MFT.
LiamR, have you tried to access your Windows partition using, say, a Linux Live Distro on USB? If you start this up and can see the partition, access it and query files on it, it might give you a chance to move off any data not backed up.
What is surprising is that (supposedly) Apple have a track record of stuffing up the .0 version and barely take a slap on the wrist. Microsoft are primarily guilty of creating two monsters - ME and Vista - and they were in the proverbial stocks for months on no end, and still haven't been forgiven for their "crimes". I tell you, the way that some Apple fanbois defend the Mac OS bastion on some of the critical articles that you see around the web... it's like a fanatical cult...
Then again, NASA stuffed up Challenger, killed a few people, no one was charged. I guess you just have to be the "good guys" and you can do no wrong...