I don't think that Prusa extruders makes much difference. Remember, it is 1:1 ratio so you'll lose the Titan's etra torque. I have one Titan and it's a quite nice extruder.
If the Titan is clicking, then I think it might be trying to feed too much material too fast and if Titan is clicking, Prusa extruder has no chance. OTOH, Prusa extruder probably has the correct distance from the gears to the hotend so it might fix the situation. However, if the problem is a too long feed length, it should be fixable with tuning the lengths in Marlin and/or start gcode. At what point does the clicking happen? Can you share a video? Also if you can share a gcode-file you are trying to print would also help.
The x-axis gong back and forth while extruder moves backwards might be by design, it kinda does that on my MMU2S also when feeding filament; first it feeds it almost all the way, then retracts few centimeters and then does the actual feed. Might be a kind extra safety move as there's a possibility of a jam just when getting to the heatbreak...