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Most commonly it will be a sensor unplugged problem. Most Ford Flashes require the rearmost EGT sensor to be plugged in. When un-plugged it will send an extreme temperature reading to the ECU and cause the truck to "limp" mode. If you are confident that all of the sensors are plugged in correctly, you may have a programming problem. When you returned your truck to stock with the SCT, there could have been a problem and left the engine, or the TCM in an unfinished condition. Did you try to program the truck the SCT will be going onto? If his has not been touched with the programmer, and still will not start, you have to have a sensor problem.
Swapping the sensors between the two trucks should not be a problem, I have done it in the past many times. If you want to be 100% sure, just stick the sensors back in the original truck to see.
If your key was on at any point during the exhaust swap, that will also cause the truck to limp mode. Some flashes require the truck to start and recognize the problem has been fixed once before it will start again. If this is the case, and you have cycled both trucks keys with the sensors unplugged do this: under the hood by the passenger side battery there is a brown wire with a light green stripe. There is a black push-connection on this wire. pinch the connector together and disconnect the wire. Turn your key on. Take the previously disconnected male end of the wire and use a piece of wire to connect it to the positive side of the battery. The truck will crank and start. Re-connect the brown w/green wire and turn the key off. Now see if the truck will start with the key.