I'd check for 12v at the battery pack I/O connector or ACM.
On my 17 pack there are 2 red wires (relatively large gauge), a purple wire, and two black wires (grd). I believe the purple wire is part of the key-on system in that when the key is "on" it closes a relay inside the pack that connects regulated 12v to the bus through the other two red wires. On mine the purple wire goes to the ACM pin 4A and the reds go to the ACM pins 2M and 3M. The blacks go to the ACM pins 1L and 1M. As you mentioned, the key has three wires all going to the ACM as well. Black to 1A, purple to 2A and yellow to 3A. If as you tested the purple has 9v and if connected to the yellow the bike starts then one conclusion is that the 9v battery is providing the power through pin 2A through the key to 3A where it passes to pin 4A which closes the relay in the pack and connects the battery (12v) directly to the ACM via pins 2M and 3M. Of course, the circuit could work the other way around as well.
Bottom line, I think you need 12v at 2M and 3M for the bike to start. If you don't have voltage you'd work back from there.