Wiring issue on 2012 IH workstar

Here is an issue that I have exhausted my ideas hoping the IH professionals have run into this before.
I actually have 2 issues which may or may not be connected and mainly concerned with the first issue.
Its a 2012 workstar plow truck with a dump body. I have lost rear signal and brake power (signal and brake on same power like small autos) I have working right front right signal and hood signal. There is a large junction box on the side of dump body and if I jump power to the right signal post lights will work so I know the rear circuit is okay. If I disconnect the cab connector and connect a jumper between the two parts of the cab connector the signals will work fine so I know the circuit from cab to rear right signals is okay. The problem happens when I reconnect the firewall plug then I loose my signal power. Disconnect and put test light on firewall plug pin and there will be no power. If I cycle the key I will again regain signal power. I suspected the body controller that is mounted on the left side kick panel to be the fault and swapped with another controller also out of a 2012 but problem existed. Also replaced signal stat no change. The thing that confuses me is the key acts like a reset is there another body controller that plays a part?

The other issue is when the key is on and you turn the wipers on the truck clearance lights will come on even with the headlight switch off. If the headlights switch is turned on and off the clearance lights will turn off and the wipers will stay on until wiper switch is turned off.

Any info is appreciated and if you need more info ask and I will try to help more.