Brake System Fault Warning

Hoping to get some help with this...

I have an 09 6.4 Crew 140,000mi, leveling kit, Spartan tuner, EGR delete, Mishimoto radiator, new AGM batteries... Strictly for mileage, I run the 275 tune daily... :laugh2:
When I got the truck the ABS light was lit. I brought to the dealer a few times and they tried to diagnose. After several hundred dollars and several hours of my time, I knew nothing more than when I started.
I bought a code reader, retrieved the codes and after many hours I diagnosed the issue to a broken wire between the frame rails routed to the front passenger side wheel sensor. I have since ran a temporary wire to eliminate the light. No issues since I did that a couple months ago.

Shortly, after making that temporary fix, this current issue showed up. I was towing a 24' Enclosed trailer loaded with ATV's and while driving the "Trailer Disconnected" warning came up. Very shortly thereafter, the "Brake System Fault" warning & Brake Warning Light came up and hasn't shut off since.
I have spent hours trying to trace/diagnose the issue. I checked the connectors on the master cylinder several times. I tried disconnecting the connectors, removing and refilling the fluid, and moving the float switch. No dice!
I removed the trailer connector on the back of the truck and replaced it. There is another brake controller on the dash "Prodigy", I have removed the extra connector at the bumper that is wired to that. No dice!
Within the last couple of weeks I replaced the batteries since one tested bad and the other marginal. I since unhooked the batteries over night and the message still remains.
I have taken it to the local Ford dealer and they couldn't give me a reason the message is on my dash.
While at a local diesel shop for a replacement Mishimoto, I had them try to diagnose it. After being charged for 2 hours, they didn't have an answer but "suspected" the "GEM" module needs to be replaced.
I have spent many hours researching this issue have tried most everything I've read for a solution and am about ready to do something stupid if I can't fix this issue without throwing parts at it.

Besides that, I need to use it to tow a trailer very soon and don't feel safe doing it without a trailer controller.

Any help anyone can give is greatly appreciated! And no matter how or when I diagnose the issue I will post my solution on here to help others...