Well after following wires all morning I didn't find anything suspicious. I ended up at the shift interrupt and I got thinking. So I did some internet research and discovered that this switch if faulty, will cause the problems I have. I found out for the most part that over time the plunger will not completely reset causing an interruption and a tow back to shore. I then contacted a relative and asked if he knew anything about these types of switches as he's an oilfield mechanic and he said he deals with them quite often. He said that it is typical of these switches to build up gunk on the inside over time and when they get hot they gum the plunger up preventing it from returning to full position which could cause the problem I am having. He said the same thing that they don't fail but they do gum up. He suggested soaking it in contact cleaner.
There's no gunk on yours you can measure it with multi meter set to ohms for your knowledge base. Usually this is related to shifting in or out of gear, worn shift cable will drag the switch and trip it cutting ignition vs causing a quick ignition cutoff/ stumble required to get the dog clutch to pop out of gear...as outlined above...
If it happens out on the water just disconnect it and see if it runs again... you changed your controller would verify when in boat this isnt tripping this switch, otherwise look else where.
What you need to do is check for spark and fuel when it cuts out other wise you are pissing into a fan... I would take it out and do laps near the launch until it happens and be prepared to diagnose when it happens.
Look for spark - if no spark probably a loose electrical connection like key switch or man over board/kill switch, or loose cannon plug.
Take flame arrestor off and pump the throttle to see if gas comes out accelerator pump. Would bring a small container of gas to dump a little down carb, if it runs a bit then dies you know you are loosing fuel and need to verify fuel supply back tot he tank...