Thanks Bill for doing some extra inquiring for me. This morning, I D/C the battery, took off the coil cover and checked the ignition connections, pulled the EHC off and re checked/re greased the serial connections, pulled the EFI controller in case the there was something in that connection. I even put a small pad under the controller connector just to make sure its seated.
Once I got it all back together, re connected the battery. Did start procedure. EVERYTHING NORMAL!! EHC lights good, turn signal works.
We got on the bike and headed into town to the HD dealer for the ride. On the way the engine still did its cut out thing. Engine light would flash on, engine would miss/cut out for a split second then come back. A second later the engine light would go off. It was running so I left it alone.
At the dealership we walked around, talked some shit and decided to go for our own ride. When I went to start her up. Key on, hit run.... Nothing!! Spoke to one of the shop guy (old school mech), he mentioned that sometimes the wiring can get "pinched" inside the hand control. Especially with the internal wiring system. So I pulled the right hand controller apart and sure enough. There are 2 wires from the brake lever that connect to the button board, they were worn to near breaking off and looked suspiciously like they were touching. They were TINY little connections. So we (myself and my lovely wife) walked of to Lowes with the parts. Brought a butane soldering iron, my pocket knife and the smallest drill bits they had (1/32? for a dremel). Them in the car park we proceeded to strip the wires off, clean the connections and re solder them back together. Actually it looks like a better job than factory. We got it back together and she started up first pop. (forgot to take pics, sorry guys)
I thought that might have been the reason for the intermittent engine cut out, but on the way home it did it again. Only once though, but once is enough.
At least the list of problems is getting smaller.
I think my next jobs as you you've mentioned Bill, will be to check more connections. Any earths or even + connections Ill pull and clean with a wire brush and see how that goes.
Slowly but surely....