At this point, I'm at a bit of a loss about what to do. My two choices seem to be either to try and grab a cheap releacement motherboard (preferably a rev2 to replace the current r1) or fall back to my old beige using either the G4 or the G3 500.

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I suppose it's just speaking the obvious to point out it'd probably be a bad idea to put that G4 module into your beige machine, unless you're willing to take the risk that it'll murder that unit's motherboard as well. I'd consider it damaged goods unless you can possibly think of some other thing you might of done to damage the B&W's motherboard while installing it.

EDIT/PS: It might be worth pulling the firewire module off the B&W's motherboard. I have vague memories of people suffering "weird" problems on those machines solving them by removing said module.