If you just re-run setup, the setup program will only change the registry settings that it sees as wrong. IE the hardware settings.
You could try uninstalling all your hardware from device manager (after making a backup) then doing the swap, so when the PC restarts it has to redetect everything, it works in win9x, sometimes in NT4, but who knows with NT5. I'd give it a shot
There is usually never a good reason for a re-format, unless the filesystem is acting up. I had a problem a while back where the setup would crash at the very end of registering components with a fastfat.sys error, thats the sort that warrants a reformat, as the last resort.
However do note that I havent figured out how you re-import your user profiles properly. If you do, tell me! Win2000 tends to make new copies with the Computer name as an extension IE Administrator.YOURCOMPUTER-WIN2000

but most data can be copied into the new profile name like favourites, cookies, start menus etc.