windows 98 will allow you to change the motherboard/cpu/mem without too much problem, window XP will throw a wobbley and wont allow it.
with win98, you will need to install the motherboard drivers from the cd. (assuming that windows will actually start), if it wont then using safe mode you should be able to get it to work. i have done this but i must say, not recently so cant be sure. If by chance your pc will not boot then maybe you will have to do a format/re-install.