The save data is stored in your '[My] Documents\SH3\data\cfg\Careers' folder. If you copy it all over to the drive with the new OS, you should be okay provided you don't make any changes to the actual game files. As for Vista/Win 7, lots of people have SH3 running on them without any issues.
If you happen to need additional help, please see this thread:
http://www.subsim.com/radioroom/showthread.php?t=162165
Hope it works and good luck!