There are a few differences in the ports and such, but the cylinders are completely swappable, you can put an 86 cylinder on an 89 engine and it will run just fine, so those differences are rather minor.
One of the major differences are the connecting crankshaft, specifically the rod length and piston. Starting in 1987, Honda used a longer rod and a shorter piston. (the piston isn't actually shorter, but the rod is mounted higher inside the piston, so the distance between the pin and dome is shorter, but the piston skirt is the same length). This is referred to as the "long rod" crank. You can use an 86 rod with an 86 piston in any motor, or an 87-89 rod and 87-89 piston in any motor, but you can't use an 87-89 rod and an 86 piston without adding a spacer plate.
The upper gears are a little higher on the 86.
The 89 had a slightly different (and better) clutch design, but there are kits to upgrade the 86-88 clutch to the 89 style.
The motors are basically identical on the outside, and you can mount an 86 motor into an 89 frame (and vice-versa) without any modifications.
Duncan Racing 340PV, +2 A-arms, +4 LSR axle, and a host of other goodies.