Can I swap out the motherboard and CPU and keep the rest

Basically, the swap shouldn’t harm any data on the disk. Windows, on the other hand, may, and probably will, shit itself, meaning you’ll have to reinstall. Burn any and all data you want to keep to CD or DVD before doing the swap, because there’s a chance it may be knocked on the head by a reinstall - it’s a slim chance, but it’s a chance nonetheless.