Alternators generate AC voltage that is rectified to DC by the Rectifier/regulator module. In rectifying the voltage a pair of diodes are used for each pole of the alternator output....one supplying current to the + output and the other, inversely wired (anode grounded), supplying the return path to the alternator winding. If you put - on the + lead and in doing so, close the loop so current can flow in the reverse direction, there is nothing to limit the current in the circuit and the - diode will melt internally causing a short circuit and if sustained long enough, something is going to melt.
The trigger coil (Stator) shouldn't care as it's a piece of wire. The Capacitor Discharge Modules have to have a holding diode at the input to the capacitor so that the charge doesn't bleed off between "humps" of the rectified AC input. Reversing that input "shouldn't" matter unless a reverse transient of sufficient amplitude were applied to the diode, which I doubt could happen. Trigger circuits in the CDM have/should have adequate protection.
Mercury tach signals are rectified sine waves and are the grey wire coming off the Rect-Reg module.
If the reverse were to burn out the charging coils, it shouldn't affect the trigger coils (under the flywheel....Stator) as they are separate circuits. However, if all the wires are bundled as they come from the Stator, and the short lasts long enough, the insulation could melt and the wiring bundle could experience short circuits between wires and that could affect performance.
Couse with no Alternator and having experienced a short circuit, bleading off battery power, what was your battery voltage when your engine was running rough after the incident? If low, recharge it and try again........with your Reg-Rect. plug removed!