Your current service routine sounds like a good one. However, I wouldn't suggest hot swapping the batteries. Given the somewhat rarity of those motherboards, I wouldn't want to risk shorting something out should you need to get in there with a screwdriver or drop the battery or something else. Really the only thing that is likely to be wonky from the BIOS is the date and time settings after changing the battery. The PRISM card interrupts the boot process immediately after the BIOS and takes over, so not much else there to worry about.

One other thing I'd make sure to check is that you remove the foam on the lid of the P2K computer case. It has a tendency to heat up and drop down onto the CPU fans, which is obviously bad, so look out for that.

Also check for blown or swollen capacitors on the motherboard. Rob Anthony does great board work should something look afoul and you don't feel like doing it yourself.

All in all, sounds like you've got it. I wouldn't let that PSU run for too terribly long without a new fan. They've been known to get a bit toasty, then as you can imagine the problem moves downstream.