I have two problems in helping you. First I don't know the scanner your using and what it can or can not do. And second it is in a Ford. So it is also going through a Ford PCM. So I am assuming your connecting with OBD 2? So I don't know what your able to do or not do with OBD2. And there are two sides to it, the Cummins side and the Ford side. Cummins don't make TPS assemblies, they call that truck builders responsibility. Plus two wire harnesses, Fords and Cummins.
I can provide you with detailed pinpoint tests tomarrow, if you give me an E-mail address and fax number. Code 091 is like 13 pages of troubleshooting. But it gives good pics and step by step directions, all your specs and such.
I agree with you on the trans. Been there many times, and fixing the engine problem cured the trans.
The rad being cold at the bottom and hot at the top. It draws coolant from the top hose, pumps coolant from the engine to the rad through the bottom hose. I could be wrong here, but a rad would have to be extremely plugged to do such a thing. My guess here is, the regulator is stuck or the seal is missing or damaged. Or the coolant pump has failed on you.
If the seal is bad for the regulator coolant just circulates in the engine and won't go through the rad. You know what happens if it is stuck shut, or if the coolant pump is not pumping.
This code is a engine protection code that will derate the engine. It will derate the engine if this code is inactive if there are too many counts. And of course automatic derate if the code is active.
The other code for the throttle, operates at a set default engine speed when IVS indicates off idle.
So at the times the TPS is not working, and your foot is into it, the engine will try to go to that default engine speed. I do not know what that engine speed is, but it is not much, just enough to get you home. So it will feel like no throttle response, no power.
Remember it takes the engine burning fuel to make manifold pressure.Cut the fuel, it cuts the manifold pressure.Put bigger injectors in there and automatically get higher manifold pressures.
So even though there could be a waste gate problem, or intake leak causing your low boost problem. It could also be the ECM derating the engine, cutting the fuel and timing back, lowering your boost.
Have you cleared the codes and seen what code came up as the problem was happening? Watched what the ECM sees for coolant temp as this low power was happening?
If you want that info shoot me a PM with your E-mail and fax.