Custom wiring is a fun exercise. It's an opportunity to simplify the works and get to know it intimately.
The amperage most of the circuits carry on motorcycles is pretty meager, and 14-16ga marine grade, tinned, pvc insulated wiring is sufficient. 12ga, coupled with relays to bypass handlebar switches, is great for headlights and ignition systems and 4ga is enough for starter motors.
I've heard pros and cons regarding solid state voltage regulator/rectifier combos, but have never had any issues with those I've used. Podtronics, Sparx and others make single and three phase units that I've used with success.
For terminals, I like heat shrink bullet terminal connectors, like the Krimpa-Seal ones. They're weather-tight and have high pull strength. My favorites are double crimp terminals (they crip the wire and the insulation) that incorporate low temperature solder in the connector. I've had trouble finding them regularly.
Hope this helps.