Well, I have more information.
I called the Tekonsha tech support this morning. They make the recommended P3 system for EOH brakes and they make the Ford IBC. They did confirm that the Ford IBC does not work well with EOH brakes but it is its own unit in Tekonsha so most information has to go through Ford (legal issues I assume).
The recommendation for the 2008 Ford Superduty is as follows:
1) Unplug the harness from the Ford IBC at the controller. They stated you need to remove the central panel section (radio/heat controls/upfitter) to get to it. They told me how to remove the central panel but before I post how to do, I will test it out.
2) You then obtain a Ford harness with blunt end wires that plugs into the Ford wire harness you just unplugged from the Ford IBC. Tech support said this new harness had to come from Ford.
3) Wire the harness that came with the P3 to these blunt ended wires.
4) You will get a warning on your information system that says something to the extent "IBC fault". I asked how do you clear the fault. You can't.
I then called Ford Customer Service which referred me to my local dealer. I called the dealer and they are researching the solution. They did confirm you will get the warning and it can't be cleared. They also said the Ford does not make the harness yet.
Both Ford and Tekonsha stated you cannot have two systems working simultaneously if you thought about just jumping the P3 into the system.
The best solution would be to find out that Ford makes this harness now and it fools the computer into thinking the Ford IBC is still there and functioning. The Ford POC is to call me shortly but I am not holding my breath on the best solution. I will keep you all posted.
BTW, on previous Ford models, all you have to do is unplug the Ford IBC back under the dash and plug in the Tekonsha harness made with a Ford end and the Tekonsha end that fits into the P3.