You will definitely be better off doing a fresh installation with a new motherboard, instead of trying to recover your old one. Windows takes note of all the onboard resources, controllers, etc. After that, you probably won't have to do it again if you upgrde your CPU or add RAM. The worst that will happen is that you'll get an error message about it when you do it.
The most important thing to do is to back up your files before you start. Probably the best way to do it is to use Norton Ghost or Acronis True Image to clone your drive. That backs up the entire running installtion to another drive which is fully capable of running in place of your current drive with no modification. That way, if something goes wrong, you can restore your drive to where it was before you started without having to re-install the OS yet again.
You can download a free copy of Acronis True Image in the disk tools from Seagate - Maxtor (same company). The only requirement to use it is that at least one of the drives (source or target) must be a Seagate or Maxtor drive.