It's going to be a couple of weeks before I can get back to where the trailer is to deal with this. I appreciate everyone's input and ideas.
A couple of things I can comment on now though. Ford confirmed the controllers in the 2017 Super Duty trucks work with all major electric over hydraulic actuators. It was noted that the braking signal was influenced by both speed and brake pedal pressure.
This unit has sat for 3 years in storage so I can guess that bleeding the brakes is a excellent idea then trying the brakes both with the truck controller and the breakaway control and see if there is any difference. Checking the brakes with the wheels off of the ground does not give a realistic test to the brake since you have no load resistance so I will do it on the ground.
I will update after I get my hands back on it.
Thanks