This is to late for the old coil but you should have cut away the plastic coating off the mounting lugs on the coil. The lugs help transfer heat out of the coil into the frame.
The Pamco with e-advance has a protective circuit that shuts down the power to the coil when you turn on the key but don't start the engine. I think it's like 30 seconds, not sure on that, now if the engine fails to start and you leave the key on the power still flows.
So now is the question, How did you shut down the engine? If you have and use an engine stop switch, there is no power flowing to the ignition or coil when in the off position.
If you shut off the fuel and let it run out of fuel, then the ignition will still power the coil.
If you use the testing procedure as outlined on here and the Pamco website for checking the ignition, you can hook a voltmeter to the green wire at the coil. If the ignition is working the voltage will change from about battery voltage to about zero volts.
Power goes to coil, the green wire runs from coil to Pamco where the transistor grounds the circuit. When grounded the meter will read about zero volts. When not grounded the voltage will be about battery voltage.
How are your coil and ignition wire? Is your bike stock with the ignition and coil plugged into the stock harness red/white wires? If so then your engine stop switch controls the power to both the ignition and coil.
If you have a hand built harness do you have the coil and ignition on separate circuits? If so then your engine stop switch may only stop current flow to ignition but not to coil.
A bit more info may help us help you.
Leo