... That said, I've noticed I have small wires not connected to anything in the case near the PRAM battery. Nothing obvious to plug them into...
Are they white? They may be for Airport. I'm presuming the little fan is plugged in right next to the battery?
I don't blame you for wanting to chuck the motherboard. If I was an Apple tech servicing this issue, I would have already tried exchanging the mother with a known-to-be-good one.
Your symptom "It also seems to mess with my display being able to wake up, unless you boot into OS 9"
might not be a symptom at all. When my MDD boots into OSX, the screen doesn't light until OSX has been recognized and started loading, as evidenced by the big apple appearing simultaneously in the screen center. With OS9 (and earlier) you typically see the screen light up first and
then see the Mac happy face / OS9.2 box as the boot System is located.
Distilling everything described so far, it appears the issue now boils down to OS9 being unable to successfully reset the boot to anything in the startup Control Panel even though it may appear to do so. Note the pic below of my OS9 Startup panel. The left-hand "Name" column shows all the drives/volumes. The right-hand "Version" one shows the bootable Systems on those Volumes. Note that I could easily have a drive
named "OSX" and select it without actually having a bootable System on it.
If OS9 doesn't "see" an actual System as evidenced by the text in the Version column, selecting that OSX-named volume is the same as selecting no other boot System at all and
the computer simply boots back into OS9 again just as you describe. So, you should be able to see "OSX 10.4 build xxxx". If you do, I just typed all of this for nothing. If you don't, I don't know why that is exactly but it does indicate something about why you can't get back to OSX without resetting the PRAM thereby starting over from scratch.
Note that the other thing I would try as an Apple tech would be to install something other than Tiger… i.e. Leopard 10.5 just to see if it works.
By now it should be obvious that a LOT of computer troubleshooting is typically done by substitution and that's easy to do "at the factory" so to speak. At home, not so much.
Note also that the other thing I probably would have tried by now in your situation would be a shock treatment achieved by dropping the whole damn thing out of a second story window.
But hey, that's just me…