Check to see if the posts in the relay are loose/wobble at all. I had a similar situation a while back and found that the post in the relay was loose and would cause intermittent problems. You can buy the relay separate from the rest of the controller and change it out fairly inexpensively.....or buy a whole new controller.
As far as fuses in the GP circuit, I am not sure, but I do know there is a fusible link in the circuit that included the green/red striped wire that goes to the GP controller. It also services the High Idle/timing advance solenoid. In my van it is located by the passenger side battery. However, when I cooked mine it made my van not even turn over and I had no power to the electronics in the cab.