if you are going to pull both engines it is much easier to pull engine/transmission combos on both cars and then make the swaps on the ground or garage work bench.

to remove the transmission as well is a few fast bits and pieces if the engine has to come out.

Keep the RPM sensor mounted on the back of the block and use the flywheel, or drive plate if automatic, from the 1991 Bertone. You'll also need to use the Coolant Temperature Sensor from the 1991 car. Remove it from the 1991 engine and install it in the earlier motor. I would also use the injectors and throttle body from the 1991 car on the 1989 engine. It would be easiest to just install the 1991 intake manifold on the 1989 engine. You'll use the engine wiring harness and Idle Air Controller from the 1991 car.
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john

I'm no expert on the turbos but I believe that the '89 model used the LH2.2 fuel injection system while the '91 used the LH2.4. Perhaps others out there can confirm.

If you stick with the '91 system, I believe that you don't have to change any wiring harness. However, you do have to swap the flex plate as you stated since you need the tone ring on it. The mount for the Crank Position sensor just bolts on - of course, that is if the '89 block has the mounting bosses.

Other differences would be the air mass meter. You would have to use the one from your '91 model.