Nice bit of dectective work. Glad the bike is up and running.
Maybe a good time for going over the wiring harness to look for other signs of "repair" from previous owner(s).
Since your playing with electrons, it's also a good time to check the first 3-prong connection between the stator and rectifier. Keeping those contacts clean is a very good idea.
The bike should run just fine with the 38 pilots....the 40 just add a bit of help at the low end for some bikes.