I had in mind to do something very similar to you ie start "nearly" from scratch - new mobo graphics and sound cards etc but utilising my existing HDDs to avoid reinstalling.
But I've just read on page 148 of the current issue of PCA the reasons given above :-
". . . replacing a motherboard involves more than just a change of CPU. There will also be a different chipset, requiring different drivers and many other hardware changes that would invalidate most of the hardware information stored in the Registry."
There is no problem installing applications on a new, or newly reformatted, HDD it's picking up all the small upgrades that have been installed since the original installation that's going to awkward.