I would not separate the gear boxes. especially the auto boxes.
The 4D56 has had a bad rap too, do a search on 4d56 problems, some are over heat, seems mitsy's need to be watched for this. clean and flush both rad & block for optimum cooling. I don't know why you would go for a smaller motor that the 4m40. The better one is the 4m41, 3.2L derived from the 4m40 and most of the problems of the 4m40 addresses. But you have the 4d56 now just make sure very thing is flushed, cleaned & like brandnew when replacing the motor.
Sorry I did not catch where you live but in the tropics don't be afraid to turn off the AC if the engine temp begins to climb, this will help immensely.