I've had 2 CB cars now, one 2.2L, one 2.5L. I was able to do a little digging thru the dealer in Tacoma, and you'll need the puter specific for your motor. The 2.2/2.5 have different fuel curves, injector firing rates, spark advance curves, AIS control, ect. in the software. Same goes for an auto/manual puter. You can use an auto puter on a manual, but it will keep looking for certain things, like the lockup solenoid. One BIG difference I noticed after the 5-spd swap(both cars) was with the auto puter, if you pressed the clutch at high RPM(over 2800), the engine would try to hold the RPM at that point for a few seconds. With the manual puter, it was clutch, RPM dropped immediately. Your car being an '88, I'd find an '89 puter. Better diagnostic and drivability software, better fuel curves, ect. This was the only difference between 88 and 89 SMECs. Otherwise, it's plug-n-play. The motor sensors, TBI, wiring harness, ect are the same on both motors.
Oh, and if your car is a Cali car, it will need to be a Cali-specific SMEC. They had the EGR control solenoid, and Federal/Canadian models didn't.