I swapped an 88 Integra d16a1 into a 86 Integra. The 88 has a different distributor and different cams. The 86 distr will fit funny on the 88 head(The mounting holes dont line up). I originally used the 88 intake manifold with 86 TB, but the EICV(Electronic Idle Control Valve-$255)was bad, so I used the 86 Intake manifold, with the 86 TB(one plug is different on the 88 TB so it wont plug into the 86 harness). I used the 86 ECU for all this
Basically, the engines are a lot different than they look. The 88 uses a newer style distributor setup, so you CANT just plug the 88 ecu into the 86. I never got the car to idle right and the timing always seemed off. Best idle and driviablility was from this setup: the 88 engine, with the 86 cams, and 86 distr, 86 TB, 86 Intake Manifold in the 86 car. If you want to use the 88 cams, youll have to hog out the distributor mounting holes to advance the timing enough to make it run right.
Be prepared to buy cooling and vacuum lines.
Basically, I ended up getting sick of the project and sold the car. I now have a Civic and life is good. Lots of aftermarket support, cheaper parts, better designed car in most repects.
Later