"It would only register 12.1 after the 50 mile ride home from where we split off and the charge voltage when running was 13.2 at 4000 rpm...That's not right, somethings amiss."
You should be running about 14 volts at 5K.
I had to replace my stator recently. I got mine at RM STATOR
They have an online electrical fault FLOW CHART
that may help you find what the problem is.
Great pics and report, hope you get your bike problems sorted.