Sorry for such delayed responses.
The ignition company sent me a new black box module as they call it. I installed it yesterday and also went through the wiring to the coils and sure enough the pigtail wire to run them in parallel was wrong. Changed that around and went for a ride without putting the front cover back on. Bike rode like a dream, 10 minutes, 20 minutes, 30, 40, 50, 60. Wahoo. Thought I fixed it. No problems. Problem solved. Got home. Put the front cover on. Ate some lunch. Then went for another ride, and after about 20 minutes. Same damn problem as before.
Well, decided to take the cover off again, went riding around and apart from a little sputtering at the beginning once the air cooled it down she rose great again.
Emailed euromotoelectrics again and tell them this, they said it sounds like The Hall Effect Sensor is working intermittently and they will send me a new one.
Other suggestions he said were to put spacers between the cover and motor to allow more air. But still think something's not rit. The front cover was sooooo damn hot when it was having problems when it was on, and with it off even e alternator was way too hot to touch. I'm going to take some temps tomorrow because John at Euro says it should not exceed 300 f.
Anyways making progress nonetheless. And have at least been able to get some rides in with this beautiful Florida weather.
Some pics from yesterday.