The ECU often controls the Torque Converter Lock-Up, like 90xj06 mentioned it might NOT on your Jeep. If the Trans has its own electronic control unit, it would probably control the TC Lock-Up, but its possible the Engine ECU still does it.
If you swap an ECU for a Manual Trans Vehicle to Automatic Trans equipped Vehicle, you could loose that TC Lock-Up. This would drive up the temperature of the trans drastically and likely damage the trans after a while. Note engine rpms at different speeds at cruise before the swap, and then check them after the ECU swap. If engine rpm is higher at the same speeds during cruise, then likely the TC is NOT locking-up, as well, a non-locking TC often makes the trans feel sluggish in many situations, especially part throttle.
Other than the TC Lock-Up, which may or may NOT be controlled by the ECU, if the vehicles that the ECU's are designed for are identical other than the trans, than the only other difference is usually some fine tuning of the fuel/spark to make the engine run smoother/perform with the trans, OR make less pollution because of the load differences with the trans. Most of the posts I've seen of people doing this kind of swap, in Jeeps and other Vehicles, don't notice any difference, unless the TC is NOT locking-up, then its like I described above.
