You will need to install a pilot bearing in the end of the crankshaft, and the spring clip that retains it. New rear main seal. (of course) Orientation of the flywheel does not matter on an 88 with LH 2.2, as it is timed from a pickup coil in the distributor. Use the transmission crossmember and complete driveshaft from the 5 speed car. You will definitely want to swap the rear axle too. The manual transmission cars came with a 3.31 and the automatics were either 3.73 or 4.10. This difference will make itself apparent (if you don't swap the rear) in quicker acceleration, more noise on the highway, and most noticeably, WORSE GAS MILEAGE. As both cars are 88s, there shouldn't be a problem with the speedometer. If the replacement axle were from a newer car, it might have a different number of teeth on the tone ring, causing an incorrect reading. While the axle is out, take a look at the speedometer sensors on both axles. If they are different, use the one that is original to the new (formerly automatic) car. If they are the same, use either one. Punch mark both halves of the driveshaft flange at the transmission and rear axle so it goes back together the same way it was originally.

SAFETY WARNING!: If you have the car supported on four jack stands while doing the axle swap, it is necessary to put at least 200 lbs of material in the back of the car before removing the axle, otherwise it can become unbalanced (front heavy) and fall off the stands.