Unless you want to buy and swap out the ecu, AFM to MAF and then the A442F trans in your rig has its own ECU where as the 95-97 A343 has the trans computer integrated in the ECU. So I have no idea where to start on that one... I do know that the A442F trans computer gets inputs from the OBD1 ECU. So if you swap to a 95-97 engine you might need the trans, ECU, MAF sensor various connections etc.
Additionally depending on what your states emissions laws are you may need an inspection certificate from the DMV for registration.
These engines are pretty basic, robust and easy to repair. I would stick with what you've got and diagnose the issue.
Here is a link to the FSM. I had only done power steering racks before my engine blew it's HG, with the FSM I completed the rebuild myself.