OK. Some clarification. The output of the alternator is Alternating Current (AC). The rectifier changes this to pulsating Direct Current (DC). You need either a capacitor or a battery to smooth out the pulsating DC to make it smooth. One of the main reasons that you need to smooth out the pulsating DC is for the regulator. The regulator reacts to the voltage that it sees coming from the rectifier. If that voltage is pulsating, then the regulator will chase the highs and lows and never be able to regulate the voltage steadily, resulting in wild fluctuations of voltage going to all of the electrical parts, not just the PAMCO. This can result in a barbecue of the electrical system...
.. This all stops if and when the PAMCO gets fried and the engine stops.
The analogy to all this is the action of a shock absorber on the suspension. If you did not have a shock absorber, the bike would gyrate up and down every time you hit a bump. The suspension would travel to its upper and lower limits with destructive force. That's what the voltage does without a battery or capacitor to smooth things out. So, the capacitor or battery acts like a shock absorber...
The recommendation to use a temporary external battery, sitting on the floor and not connected to the bikes electrical system to power the ignition system for the initial start of a PMA system is because the PMA will do one of three things on initial startup:
1. Nothing. No output. (Capacitor setup) The engine won't start because there is no power for the ignition system. You will break your leg trying to kick start it.
2. Start on the first kick with the voltage zooming to 20+ volts, frying the entire electrical system and boiling the battery or blowing the capacitor across the garage...
3. Start on the first kick and work perfectly, producing a steady and reliable 14.5 Volts. (Yeah, right.....
)
So, if you have an external battery powering the ignition system the engine will start and you can quickly check the voltage on the bikes battery or capacitor. If it is zero or 20+ you can keep the idle low and trouble shoot the problem, including disconnecting wires without the engine stopping. If you have a battery setup, then shut the engine down immediately if the voltage exceeds 15 Volts. With a capacitor, you can continue to troubleshoot as long as the voltage does not exceed the capacitors rating, like, 25 or 35 Volts.
I also suggest that you wear an approved set of safety glasses for the initial startup.