Hey Lee, I'm wondering... I was able to cram that big 6 point connector through the original slot for it, despite having one of Tony's RRs. It was a bit of a 'different' fit, but it all held together and keeps things tucked in nice 'n neat. Might help you avoid this in the future.
12.5v at 2500 sounds about right. Make sure you test as you go up to 5k, maybe have your wife hold the probes while you crank the throttle. Make sure you max out around 13.9-14.9ish just to be SURE you're makin' juice, but that definitely looks like that would've been the problem.
I think we all have our "I think I did it!" moments only to be followed closely by "Ooohh. Didn't do it." moments. My bike still starts slow sometimes despite a full battery so that bears more investigation. ...and here I thought I had it, too, by monkeying with the start button's wiring.
Glad you found that, though! Lucky that you have the extra connector, too!