Changing motherboard is a huge issue from a Windows point of view, and changing from AMD to Intel is an even bigger issue as they both work fundamentally differently - think of it like moving to a new house at the other end of the country, you can't complain because your normal route and number of steps to the corner shop now doesn't get you to your new one!
Depending on just how incompatible your outgoing and incoming motherboard are, there is a chance you might be able to fudge your current Windows installation into actually booting, but as the others have said, I would STRONGLY advise against this. Bite the bullet and install a fresh Windows now (as Spoffle said, you don't need to format and lose your documents) and you will save yourself a lot of hassle later.
I repaired a PC for a friend of friend when the motherboard died in his 6 year old High Street Shop special offer PC. It wasn't possible to replace like for like, so I put in a new motherboard and reused all his other parts as he wanted to keep costs to a minimum. I stressed to him I needed to install Windows, but he flatly refused as he didn't want "the hassle" of reinstalling his programs. I got the PC booting eventually using some of the tools on Hiren's Boot CD, but told him this would be temporary and it would need a fresh Windows. A few weeks later he contacted me and complained that it was blue screening sometimes, generally wasn't very reliable, and he wasn't happy. I reminded him about reinstalling Windows and asked him then if I could do it, but again he thought that was a lot of hassle and inconvenience and felt there must be something else I can do - so I told him I could try a repair install, but I wouldn't expect it to be much better. Few more hours of my time and he had his PC back, slightly better but still not as stable as I expect a PC to be. A month later I found out on the grapevine that he'd bought 2 brand new iMac's for him and his wife (!) and was spreading the word that I couldn't repair PCs properly and had left him with a poorly working computer that I didn't know how to fix. Some people!
Anyway, the moral of my little ramble is for such a major change as you've done, you really are better off setting Windows up from scratch. In the long run it is actually less hassle than trying to run with an existing Windows install, and there are very few things more frustrating than an unstable or unreliable PC. As wise men say, do a job properly, and you'll only do it once.
