First, know your form factors for motherboards.
CoolerMasters make great cases for cheap. Server sytle cases. Will fit any board you can throw at it with room for seven hard drives.

When you change the motherboard, read up on the processes. The static electricity in your body can fry the board just by touching it. Plug in the power supply, run a wire from the computer case to your wrist, this will ground you out and prevent the static from killing your board.

The only advantage I have seen for 64bit is its ability to use more than 3.5G of ram.
If you don't need more ram than that, you don't need a 64 O.S.

You shouldn't have any problems, but I have run into such problems in my work.
Example, User with 64bit laptop Remotes into a 32Bit computer and wants to print from the Remote session to his local printer.
Due to the different drivers, this was impossible. So be aware of the apps and drivers you will require, and make sure they are supported by 64bit.