Chalk this whole mess up to MS and their decision to use the hardware as a copy protection measure. Go write them a letter and let them know that since you are not an idiot when it comes to computers, you like to change/upgrade your hardware every few months. And that now as a result you also need to reinstall their OS each time you do it.
Well now that I got the rant out of the way, its probably best that you reinstall the OS if you change your motherboard anyway. I have changed my motherboard about 8 times now and have always seen a performance hit if I did not wipe the OS and reinstall it. Too many things are install/configured based on the MB chipset. Its just best to reinstall to fix all the problems. You might be able to just do a recovery install, but I havn't actually tried that, simply because it was usually time for me to wipe the HD anyway and reinstall from scratch, but since I keep current backups of all my data, I never mind doing this. Takes me about 4 hours to completely wipe my drive (low level format) and reinstall and recover my data. I tend to do this once every 6-8 months just to really clean up the HD, cause windows defrag sucks, and I don't feel like paying for a decent defrag that knows how to actually run and not stop/restart every 30 seconds because of some other windows activity that "needs" to be done.