I don't pretend to have the whole answer, but you are on the right track verifying the signals to that junction block. First, verify the correct signals get to the connector in the engine compartment on the correct wires. Then, trace them from that point to the signals. I sounds like you have a wire crossed at some point. You must use a factory service manual to determine this. Here's why:
Mine is ostensibly a 1986 "GT". When I read the VIN, it did not indicate "GT" but "Special" in the type designator. The lights did not work as they were supposed to. The FSM showed a very small detail in the wiring under the dash that differentiated how the lights behaved. This jumper wire would only be present on an "SE" model. I snipped the jumper, and things started acting as expected. From this I gather that it wasn't a true "GT" model, or was changed at some point in the production process. Yours may have had the same treatment.
Also, be aware there are TWO flasher units. The hazard flasher is under the steering wheel, and the standard flasher is buried under the passenger side of the dash (it has been a while, I may have these reversed). Both use the same flasher unit, and if they are different, it can cause problems like the flashing stopping when the brakes are pressed like you describe.
Tuesday, September 9th, 2008 AT 2:45 PM