If you wouldn't mind playing tester for me hehe, could you try a clean install of RO with the new file system allready in place?
IE: Deleting everything RO related, going to steam, right clicking on RO and deleting local content, killing off the prefetch files again (if they got recreated) and deleting the new common folder (where RO sits with the new file system). And then running CrapCleaner again (but make it only look for out of use registry keys, and have it clean those up).