I just did this when I upgraded from my ATI chipset S939 board to my Intel chipset S775 board. All you have to do BEFORE YOU SHUT DOWN is delete any drivers on the motherboard. Delete the LAN and sound drivers, and change the SATA/IDE drivers to windows default. At this point you can shut down, swap boards, and boot up again. I had to wait quite awhile while it loaded the new USB and other drivers, but I didn't have to spin any disks. The repair install will work, just takes longer. It took me maybe 20 minutes to change the hardware, and another 30 or so to load the drivers. Something to keep in mind for next time.
BTW, as long as you don't change "brands", you shouldn't have to do this. All chipset manufacturers went to their own standard drivers awhile ago. As long as you stick with one, you shouldn't have to worry about changing motherboards.