|"I now have a fat32 instead of a ntfs and my files are obviously gone"|
Boot record can not change the file structure.
I'd start with getting a live cd and boot to it just to see what files and partitions are on it.
Then decide if you have selected the wrong partition or what when on. Might be you are looking at the recovery partition.
"Best Practices", Event viewer, host file, perfmon, antivirus, anti-spyware, Live CD's, backups, are in my top 10