I am looking to upgrade my motherboard and processor, but I will still be using the same PCI cards and other devs.
I have gotten my Ubuntu 5.10 install configured exactly like I need it, so I don't want to reinstall if possible.
I probably won't move up to a 64 bit cpu yet. (Both old & new cpu's would be 32 bit)
Would there be any issues in just switching out the mobo and cpu?
What would I possibly need to configure or re-compile?

Welcome to LQ!

Generally speaking, No, you probably won't have any issues switching the mobo and CPU. The one caveat however is whether or not you plan to use any of the onboard devices (sound, video, LAN, etc). If so, the new mobo may use a different chipset than the old one, and thus may require different kernel modules be present. That's not necessarily a problem, but it is something to be aware of. That said, assuming you stick with well known brands, it's unlikely to be a major issue.

If you are using standalone cards, and have no use for the onboard devices, then a mobo+CPU switch probably won't require any configuration or compilation actions. Good luck with it.