As sky stated, hardwire is the way to go, just put quick connectors on it and bada bing! Make sure you have a solid ground, as well as all other connections too. Definitely sounds electrical to me.
And as far as a break in period goes, I put a new used engine in my R this spring, the day before i had my first ride planned, it was a ct310 that had been sitting for a couple years now, but ran great last time it was run. I put it in, had gas, spark, air, but no fire. Ended up pulling the top end to find the rings frozen and no compression(i had done a compression test and it was at 70lbs, but it was an old tester and i wasnt sure if it was accurate, but it was!). I put a fresh top end that just had a bunch of port work(RB racing aggressive drag port) and head work done to it, on the 310 bottom end, rode it up and down my road 3x before church, came home from church and went duning. I took it easy in the dune 1/2 dune entrance and kept it jetted rich that day and the next ride. I am a firm believer in breaking it in hard, but rich. I only went down 2 jet sizes from there.