OEM means only able to be used on one machine. Changes such as a completely new motherboard generally mean buying a new version of windows. However it depends on the rep on the phone as to if they make you get a new version or not. Usually calling microsoft a few times once it asks for you to call them about it will get it sorted. Alternatively I have heard of people saying to them that all that has happened is the addition of a new hard drive has brought this message up for no reason.
Not really what you are meant to do. But I always took it that as long as over 50% of the computer was still there ie ram, hard drive, case etc then it should still be the same computer. Motherboards fail and need replacement.
There is no difference in the versions bar that the full version you can install on another PC. But only have one copy of the OS. But it is transferable to new PCs you may get. Useful if you buy a new PC often to replace an older one but OEM is generally sold to the likes of Dell PC users.