The problem ended up being the brand new brake module. I ordered the service manual specifically for this truck.
Something I would like to point out to anyone having this problem is that the service manual is wrong about input test point TP5 when it says that if there is not any voltage to TP5 that the problem is in the circuit, wiring, components before the brake module.
The module supplies voltage to the K3 relay which then goes back to TP5 to energize the brakes. It was not supplying the voltage the second time do to the brake module itself.
Hope that helps anyone having similar problems and is something to remember.