2005 cummins, auto (48re trans), 4x4

New trans rebuild 3500kms ago

Tow/Haul flashes on and off, every time it does it'll shift in and out of overdrive, when on highway.
I first called the shop(@500km), he said it was probably the wires coming out of the shift lever in steering column. I checked this and it was fine, I even disconnected this to eliminate it potential switch/wire issue, no change
Shop reccomended to cut a wire coming from the ECU that is the TH switch signal. I reluctantly did this and the engine ran horribly, and had no power, with a check engine light on.
I reconnected the wire, and headed to a near by shop (Mr. Transmission) and they scanned for codes and the one that caught our attention was the Accelerator Peddle Position sensor (app sensor) this came up twice, so I bought a new one.
The problem persists, and I am 3500kms away from the shop that did the rebuild, He is claiming that the ECU is failing.
I discovered that the TH flashes only when I take my foot off the fuel peddle, coasting and/or decelerating.
Every time the TH flashes (rapidly on and off) the trans shifts in and out of OD until I can carefully get it to stabilize with a load on the engine and it''ll operate normally until I get on a downgrade where i need to lift off the fuel peddle the the TH starts flashing (on/off randomly) again.
Now that my 5th wheel trailer is unhooked, I can't drive the truck since there is hardly any load!

Has his happened to anyone?

Thanks