Just a follow up update to this thread, as I have a Simpsons cabinet, and I wanted to play TMNT in my cab as well.
My harness for Simpsons did not even have any pins in the plastic JAMMA connector in the positions for mono audio (positions 10 and L). So I grabbed a little 4 pin connector that mated to the one from the Simpsons audio connector, and soldered some wires to it. On the other end, I crimped edge connector pins and slid them into the connector housing. Now when I want to play turtles, I unplug the simpsons audio connector, and plug it into my little pigtail connector that hangs off my JAMMA edge connector. Works great.
To get sound out of both speakers, I wired both negatives (middle two wires) to pin L (solder side) and both positives (outside two wires) to pin 10 (component side).
I'll grab a picture later to illustrate what I'm talking about.
I'm also considering adding some quick disconnects to the inputs for attack and jump so that they map to the correct buttons too. That way when I change boards I can simply flip a few connectors and the buttons will be correct for the TMNT board. (they are reversed for TMNT)