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i had the exact same problem a few years ago and it turned out to be bad wiring to my battery GND terminals (or 12V) cant remember. Either way it confused me a lot until i actually traced it all from the battery to its relative places and found some crap wiring. Upon repairing, the beast was perfect again.

edit: with my problem, obviously, the entire 12v rail would be gone. everything would cut out, incl the engine.. lights, dash lights everything..
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I will follow wiring to see if that will do the trick. The wiring around the battery looks bad. When you say everything would cut out do you mean it would totally die? My motor keeps going like it going to stall but then it goes right back to normal. I don't need to restart. Let me know please:)