You seem to already be going ahead with this, but if I had caught you earlier, I would have suggested backing up data files to DVD or another HDD, then do a full clean install of XP on a new HDD and copy the data files over. The down side to this would be that any applications would need to be reinstalled, but this is the only real sure way. As per having my own problems in the past, I store my data on a separate HDD than the one the OS is on. An extension of this concept is to install your apps on a different HDD than the OS as well, but this has limited benefit.
PK's recommendation for the future: Install OS and Apps on one HDD and set up your data directories on another. Include a directory on the 2nd HD that has all of your DL's (app DL's for instance) which will make it easier to install your apps if such an event pops up again. For thouroughness, I also copy my entire MAME directory, even if the paths dont match, they can be made to match.