This is a really strange problem. Boards are ruled out and there are funky switch matrix issues.
There seems to be an issue related to the switch matrix and that switch 88. I was wondering what would happen if you removed those three switches from the switch matrix, which are mounted on the subway ramp. Just pull the connector.
When doing the testing, is the mini playfield in "home position ? Can you connect the 12VDC supply to the motor and set it to the highest point of travel and then re connect to the game and observe ?
I had a similar issue AFTER installing the two cliffy's where the front of the mini playfield jammed against the playfield and simply never moved up or down. I had to loosen the assembly and move it back and it worked fine proving the problem was physical. I know you mentioned in your original post that you have connected a 12V source and it does work, but was it while the mini playfield was in the game or on your bench ?
