The square plug on your eng harness that doesnt match the body one is the B1 plug (in tsrm).
89 cars used both styles, the 87-88 and the 89-90. Early 89 built before 1/89 is square and after is the other which is more rectangle.
You will need to de-pin one of the plugs and use the correct one. Make sure you use the pinout diagram and dont mix them up.
I recently did a 89 ge to gte and ended up using an 88 eng harness and repinned the plug because the 88 b1 plug had wires in different spots.
I might have the B1 plug if you need.
Rich