I just went through all this!! Got the new head unit in no prob, without the 3rd plug.. but getting the factory amp/sub to fire up some bass was a whole different ballgame! I had my other half out there with a voltmeter checking all kinds of stuff... we had to go to Radio Shack and get some kind of resistor too... it took him the better part of ohhhhh let's be liberal and say 8 hours lol
I'm sorry, I have no good advice to give. It's a major pain in the rear to hook up an aftermarket head unit to the factory amp/sub is all I can say. But it can be done! I'll see if I can ask the old ball and chain exactly what he did, and providing he actually remembers I will get back to you.
I share your frustration though!