You state you have two wires coming out of the mag. Normally an FM J does not have any wires coming out of it other than the kill wire and the four plug wires. Under normal circumstances there is a wire connecting from the points to the kill wire terminal. This is nothing more than an insulated brass machine screw that goes through the case wall. On the outside of the case there is a wire connecting to a kill switch. Grounding this terminal is what kills the tractor.
If you have an additional wire coming out of the mag then somebody has rigged up an external coil or possibly an external condenser.
Where does that other wire go??