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.

You should be ok with a simple swap and let Win2k take care of everything 4 u. In most cases it will work fine. Only if there are some diferences that WIn2k can't find will u need to re-install.
Back your stuff up just in-case and just do a swap. If your system will be having some wired IRQ problem then re-install will most likly solve it.
Win2k in general is much better with HW swaps then 95/95 and can usualy handle it without problems.

There's a knowlegebase article at support.microsoft.com that talks about how to do this. Its called "Moving Windows 2000 to new hardware or something like that." Most people get the dreaded Boot Device Inaccessible message when they try to just let Windows 2000 handle it.