kilowattcommando:
First, the arduino will be running a PID loop, regulating the system voltage to 13.5VDC, by firing a PWM pulse on the gate of a MOSFET, supplying excitation current to my alternator.
On cars this is normally done using a simple analog control circuit built into the alternator. Don't bike alternators use the same approach? Without some kind of voltage regulator it wouldn't be safe to use an alternator. Doing this digitaly using a microcontroller and PWM controlled MOSFET feels like using a sledge hammer to crack an egg.