You could if they use same switch mounting.
The point about cutting connector is this. If the junkyard TB was changed for the later 2003 one then you MUST cut the connector, as the later one is different and requires the later 2003 ATX TPS switch which IS available. If you cut for convenience of removing a 2001 part at the junkyard, well, that is not the same thing at all. Or, you still have the old stuff and no ATX TPS available for that one. In short your junkyard trip did nothing at all except drive you crazier.
Ford originally changed the TB because they got a rash of fails with ATX TPS that read too low and caused trouble, note your code. You're there. Why I set the MTX TPS at .9 volts, it gets away from the low volt issue to help. As soon as TPS goes over one volt, the PCM starts signalling to ramp up injectors for increasing load, why if the idle volts are at one volt plus you get all kinds of issues. PCM thinks you are not at idle anymore and screws things up.
You must be b-tchy about setting that voltage at idle, since PCM demands it. Now, if you could get ATX TPS, then it is preset to already do that, but it's not available any more. Thank Ford for that one, and should be enough frustration for you by now to look at another brand next new car time. Simply no excuse for what they did there except greed. The switch could've easily been recalibrated to make ATX switches by the millions. But no, they force you to rebuy a part that has nothing wrong with it to get the one you need. I don't like doing business with companies that do that stuff. To begin with, totally stupid from the getgo to design the TBs with different TPS indexes to begin with, there was no need to use different TBs based on trans type. They should've used same TB and TPS on both transmissions. Or more stupid there.