Correct. I found the same problem. AE86 gearbox crossmember did not bolt up, I had to use an AE71 gearbox crossmember. If you are handy with a welder or grinder it shouldn't be hard to make one or get some 4x2 steel tube and use that.
AE86 tailshaft wont work, you need an AE71 tailshaft. If you find that the end can actually bolt up fine, slot the holes on the centre bearing to slide it further forward. The output shaft that slides into the box should be able to move further forward.