I've not read this thread till now. I read it all.
I have a few comments.
1. The schematic on the mainboard clearly shows a
balance control.
(either this schematic is of a different unit or our units may have a pot on the mainboard somewhere)
2. The idea that the old hardware is "crappy" is a fair assessment albeit harsh given it's design age. Hib can be harsh but I'm sure he meant not to be insulting. It's just that things have progressed. So far I find what we have as stock radio/amp etc adequate. I just am not too interested in the radio too much when I drive THIS

CAR
3. The schematic in previous posts with give alterations has a few problems. the L and R end up getting swapped and the ground (as was mentioned) is missing on pin 1 of the added connector. Any battery powered unit (cell phone etc) will have problems getting a signal to the car. If a charger is plugged into the battery powered unit then ground is provided and would likely work. But this method can be dangerous to the portable unit as well as inject unwanted noise.
In no way meant to insult but just as a possible improvement I have altered that diagram. Here is my take on it. Note in
BLUE is the added ground and the L side (
purple) is maintained through out as is the R (
green) .
If I can get a copy of the full schematic I may be able to come up with a way to safely power down the CD while the AUX is being used.