I removed the auto gearbox in my 2018 LDV G10, to get the worn out torque converter reconditioned. After reinstalling it the motor backfires in to the inlet manifold.
It’s a bit hard to imagine how removing and replacing a transmission could make an engine misfire or backfire. Unless, that is, you’ve managed to bump part of the engine’s electronic controllers, wiring, sensors or even something as simple as pinched or displaced a vacuum line somewhere in the engine bay. Incorrect ignition timing can make an engine do this, but, again, that’s nothing to do with the transmission.
It could even be a complete coincidence. But did the vehicle sit for any length of time while the transmission was being fixed? You might find the battery has discharged over time. Modern, electronically-controlled engines do not like low battery voltage and can run poorly as a result.