Frame:
Shock mounting width (narrower on 88).
8mm bolts on top subframe mount (88) vs 10mm on 89.
I think the linkage mounts are narrower on an 89 vs an 88.
Swingarm:
88 has slightly different drop outs for the rear axle.
88 has a mounting tab for the plastic rear caliper protector (89 is mounted to the caliper).
Again, I'm pretty sure the 88 linkage is wider where it mounts.
Basically, if you have an 88 main frame, then you need matching 88 subframe, swing arm, linkage and shock.