The Bachmann "shorting" plug for DC (as shipped) is more complex than the "old style" one that just jumpered J1 in the socket.
Most of the time, the issue is that you have to SEPARATELY provide power to the main board, to power the logic that switches the other lights.
But of course, the QSI you are using pre-dated the Bachman version of the socket, so J2 (where your other lighting is controlled) was not addressed.
(you note that the electronics connected to J1, front headlight, rear headlight do indeed work). This was the situation with the later model K27, C19, etc.
I would take a look at the QSI Titan pinout and see how many of the Titan function outputs match the Bachmann socket.
OK, on the Smoke, the Magnum never controlled the smoke, but the Aristo socket was designed to connect pins 5 and 8. Clearly the Bachmann socket has changed that, and has a logic input on 8 only.
The QSI Titan will control pin 8 on J1, but it will pull to ground, the Bachmann documentation does not give the logic levels for pin 8, but should work if properly designed.
Likewise the Titan has more than enough light outputs, and they are available on J2 pins 8,10,11,12 and on the 3rd connector, but the pins are not exactly the same.
It would be easier to use a Titan, then use the Bachmann adapter board and just use the default Titan terminals, since the Titan has screw terminals that accept the Bachmann wires.
I applaud you sticking to it.