Hi John,
if it were mine I'd rip all the aftermarket electrics outa there and put stock parts back in.
But what can you do with what you have?
I'd suggest that you connect a battery to your system in place of the capacitor, disconnect the PMA
and troubleshoot the ignition system to see if it still works on 12 Volts after trying to swallow 22 Volts.
After you know that the ignition works you can try to troubleshoot the charging system.
And yeah, take that capacitor to the river and use it to test your throwing arm.
Batteries are better.