Limp mode, codes P2104, P2107 and P2110?

Hello, what brand TPS sensor did you put on the throttle body? Ford had a lot of issues with the throttle body TPS sensor from 2004 and up. There's a really good video on these 3 codes and why it sets them. This will help, most likely you have a faulty TPS sensor even though it's brand new. Check this out and it will show you if you have one of the faulty manufactured sensors:

https://www.youtube.com/watch?v=8P3hOxDfCRo

Do you have the square looking throttle position sensor on the throttle body? And do you have an 8 wire Pedal Position Sensor? What color is the smoke coming out of the exhaust?
If you have the 8-wire sensor on the pedal, there are (2) 5vRef wires, (3) APP1, APP2, APP3 signal wires, and (2) Grounds. You are correct that APP1 should go from 5v to 0v, APP2 goes from 0v to 5v, APP3 goes 0v to 5v.
The 2nd diagram shows the Sensor on the pedal and which pins should have a signal and which will be 5volts feeds. But if you're not getting any other codes right now, concentrate on those. The video I posted, he is a Ford tech, so I would at least check what TPS you have on the throttle body,
If you have a lot of white smoke pouring out of the exhaust, that points to a Fuel Injector being stuck open.

The ECM won't learn any idle speed or pass any IM Readiness Monitors in Limp Reduced Power Mode. You can verify the voltage readings on the Pedal Position sensor and make sure they're correct. This is all that is listed in service info for these codes. You might consider trying to get a 4th generation TPS sensor for the throttle actuator from the dealership. Below is only real verified fixes, and I don't think replacing the ECM is the answer. Doing a back pressure test at one of the front oxygen sensor locations is how to verify the Converter is not restricting the exhaust. 1-1.5 psi max on a back pressure test if you think the Converter is bad, also checking the oxygen sensor voltage levels is important. But addressing the current codes would be first. Pull the air intake tube off and check if the throttle plates move with pedal movement, on a drive by wire system, the ECM is actuating the throttle plates.

https://www.2carpros.com/articles/how-a-throttle-body-works

You changed the shut off on the throttle body? How many different shut off sensors have you tried on the new throttle body? These codes are kind of all over the place, P0122 and 222 only give a Symptom description of "Throttle/Pedal Position Sensor/ Switch A (P0122), then Switch B(p0222) Low Input. So, it's not clear if this is related to the pedal position sensor or the throttle position sensor on the Throttle Body that gives the ECM the position of the actual throttle plates. And with all the switching around here, the ECM has yet to probably even learn any idle speed. The problem is that within the year range of that Gen1, 2, 3, and 4 TPS sensors having manufacturer issues is that there are so many bad sensors out there now, even if you get OEM, they want to get rid of these bad sensors, or they're not aware they are just giving out bad throttle position sensors, I have dealt with this exact issue myself on an 04 explorer. I posted that video to show you this is an issue with many vehicles. I assume you have a scan tool, and that's how you're picking up all these codes. Do you have a basic OBD2 scan tool, or what kind do you have and can you access live data PIDs? I know you mentioned voltage readings on the pedal sensor, but I would back probe the throttle position sensor that monitors the throttle plate movement, check them one at a time using the Pink/Orange wire as Ground, comparing the voltage readings from the scan tool to a multimeter. Graphing the TPS if you have the option to. With just the Key On you should see movement.
There is a Technical Service Bulletin on this as well which includes a PCM reprogram (updated software). It also includes a TPS kit with an updated part number.
Dealing with this last time, I believe the vehicle was setting a P2135 code, which pointed to the shut off voltages A/B correlation not being correct. But even on an oscilloscope things looked okay, on that vehicle the throttle body was replaced by another tech and that resolved the issue for the most part, but I would follow this TSB. You have exhausted all other possibilities except a wiring issue or faulty PCM. But I wouldn't replace the PCM without trying updated software, you may end up in the same place. Ford set a TSB because they have seen enough of these to issue a PCM update and new shut off kit. It might be the only way to resolve the issue permanently.

A dealership would have the latest software updates for any Ford products. Modern scan tools can copy information such as Vin numbers and EPROM data to new PCMs, But unfortunately the dealership is the only place that will have whatever they corrected in the software. But its better than buying a new pcm, that will most likely not have updated software anyways. So I would try that before spending more on throttle position sensors we're not even sure will fix the issue. I am sure there are other updates for your pcm you havent even heard of, there always are updates on something with every manufacturer. Print out the TSB so they can see the updated part number as well. That way they know you need the software update too. Hopefully that will resolve any issues, and if it happens to be a wiring harness problem, have them call you before they proceed with any repairs. Im sure you would want to do your own wiring repairs if thats part of the problem.