Is the coil you installed a true 12 volt coil? There is a difference, a true 12 volt coil will handle 14 volts. If its just a standard 12 volt coil, there only rated to run about 10 volts ie like the stock coil with points ignition. NAPA IC14SB, Autozone LU800, and BWD E40P are true 12 volt coils rated to handle 14 volts. I installed the NAPA with my electronic ignition and had to add a ballast resistor to keep the voltage at the coil down below 14 volts. My electronic ignition requires 4 amps or less or it will fry. Voltage/Ohms=Amps (14 volts divided by 3 ohm coil equals 4.66 amps and overheating coil). I ran an additional wire from the key just for the coil, to get steady voltage. I too, was having problems with coils overheating, and was seeing 13.5+ volts on the resistor wire. My coil is still mounted in the original spot on the engine, and I put the ballast resistor over by the reset button in one of the pre-drilled holes.
My boat would run for an hour, sometimes less and sometimes more, start to bog/miss and then only run at idle till it died.
If your getting 13.5 volts at the coil I would add a 1 ohm resister and go from there.
Your currently~ 13.5 Volts /3 ohms=4.5 Amps.
Add 1 amp resister 13.5 Volts /4 ohms=3.375 Amps. Even at 14.7 volts/4 ohms=3.675 Amps
I say add 1 ohm of resistance. And buy a new coil to put on it once you get it right. I wouldn't trust a coil once its been overheated. Its suspect to weakness in my book.