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The trans computer uses the 3 sensors for combined input. Anything being a bit off can affect the shifting. Since you swapped the motor I would think the tps could benefit from alignment. I believe the engine speed sensor signal is counted as pulses. So slight voltage variations may not matter...
The output speed sensor on the trans is a common failure item. Sometimes it will be a bit off and not throw a code. It's an inexpensive easy part to replace.