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Okay, so here is where we find ourselves.
The stator and the rectifier were both bad I replaced them and now I am getting 14.4 volts as I should.
I took the bike to a mechanic shop and he figured out pretty quickly that only the front cylinder was popping. He replaced the spark plug wires with a set of Harley-Davidson wires and the popping stopped.
This is where we start uncovering other issues. He put the bike on a scanner and checked all of the systems. What he found was that The air intake sensor was reading 200°, the throttle positioning sensor was sending little to no data or it was sporadic and it was not receiving any information whatsoever from the engine temperature sensor. The bike currently runs and starts however it now stalls during idle but runs fairly well on open throttle except when you dump the throttle and the bike starts popping ferociously. He told me that that is as a result of the TPS giving incorrect data and therefore not giving the bike the proper amount of fuel. He also tested my coils and determine that they were working very well.
He currently believes that those three sensors are either bad or that the ECU is bad but mentioned that there isn’t a proper way of testing the ECU to determine if in fact it’s bad.
This is the current state of things, does anyone have any thoughts?