Your old reg/rec, it worked with the stock stator and rotor? If so, the blue from the ignition was the voltage sensing wire. It told the reg/rec what your battery voltage was. On your new reg/rec with the PMA it wont be used. It could be used for something you want powered just when the switch is on, like an accessory socket.
The orange wire was power to the brushes, the voltage on this wire was controlled by the reg/rec. It "turned on/off " the rotor. It won't be used on your new set up. once you remove the old reg/rec you can remove any wire in between or just leave it. No power will flow in it. You could just cut it off as close to the harness as you can and leave the rest.
You are using a battery, I would use a switch, key or toggle between the battery and the rest of the bike to keep the battery from going dead from the ignition or lights when the engine isn't running. If you use a cap you can just use an engine stop switch to "kill" the engine. Flip the switch "on" then kick and go.
I would leave your wiring intact, just add in the PMA wiring as needed. Three to three and hot to battery +, ground to battery -.
As I have told others, I have little experience with the PMA conversions, I understand them but no hands on experience.
Hugh has done this many times. If I have erred on any of this he can set us straight. Hugh?
Leo
