I think the shunt is used for the diagnostics. The regulation voltage lead cones thru the cab power panel, which goes thru the polarity box. Although the fuel solenoid is a better connection, it’s still from the same source. If you are getting an intermittent drop in voltage at the panel, and the regulator senses it, and tries to bring the voltage up, and then a second later you have an over voltage situation and the alt shuts down. I would bypass the polarity box. You can temporarily run a fused/breaker protected wire from the 24v battery connection over to the regulator 24v connection. Take the lead that’s on there now off and tape it up, at least for now. See how it goes with a direct connection like I have described. You will want to pull the fuse when the truck is off since this connection won’t be disconnected when you shut the truck off. See what happens.