PeterH:
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.
The voltage regulator/rectifier unit is actually under the seat on this bike. There's a five wire cable running from the alternator (three phase AC and DC excitation)
It is overkill I know, but hope to have the controller for other features later on, so why not just start here, and just add new features as modules? I also want an LCD display with some basic OBD tools, such as battery charge/discharge rate, system voltage, alternator current, spark issues, as well as more important driving tools, like a compass to display your heading, average speed, distance travelled, clock. Easiest way to get all this information is just let the microcontroller manage it from the start rather than interfacing it with a different system.