Hey Mayoman - Just guessing but you may have located the second alarm. The MTX audio amp supplier also produced car alarms at one point. Perhaps if you can locate a part number they can provide a functional schematic layout. In the worse case scenario you will have to trace your wires back to see where they cut into the wiring harness and try to reconnect any spliced connections.
I had a similar after market alarm problem on an Audi Quattro one time that chased me around for about two weeks before I had everything sorted out. The company that initially designed the circuitry was no longer in business or had been bought out by another outfit. It had been a multi-logic unit that alternately flashed the lights, blew the horns and disabled everything but the cigarette lighter when it went off....
Good Luck, Michael