Better to err on the safe side. I'd tape it off, and be sure to tell the DMV and the Trooper that you changed the colour.
Excellent colour choice, BTW.
On the wiring: I wouldn't change much. Take the time to swap the flywheel and stator plate from your existing engine to your new engine, and everything should be painless. The new engine is not likely equipped with a lighting coil, so the original stuff is a better idea.
Also, if the ignition currently consists of two wires twisted together, it should be very easy to pick up any old keyed switch from a China bike parts supplier, Tractor Supply or JC Whitney. Like this one:
http://www.jcwhitney.com/all-purpose...wx?filterid=j1