have the same wiring setup except i went 4ga from alt to 150circuit breaker and 4ga from breaker straight to pos. battery post, 1ga from pos. battery post to 200amp breaker, 1ga from breaker to cutoff switch. 1ga other side of cutoff to solenoid. and 3/0 welding cable nfrom bellhousing bolt straight to bat. neg post. 1990fox with 3g 130amp 1 wire.
I would say try to run your alt charge wire to battery and not cutoff switch? something to try anyways. good luck!
2011 PLatinum 5.0 F150
2008 King Ranch Expedition
1990 Gt Dss 306, afr's,faceplated tko, v2, meth, all tubular ,custom paint. Dez tuned