Help "Rebuilding" a Mac Pro G3?
I don't know what motherboard setup they used, but it might be ATX. Can you post some images of the innards and the backside? Then we might be more able to say what would be doable.

(Edit: it'd definitely possible: here's instructions from someone doing essentially what you're talking about: http://www.inventgeek.com/projects/p4mac/OverView.aspx.)

I have a Sawtooth PowerMac G4 and it has a fairly standard ATX motherboard. I'm planning on pulling its innards out and putting a microATX board in there. I'd recommend getting the ATX specifications and a ruler and seeing if all the holes are in more or less the right place. So what you're thinking of is definitely possible.