I'm not sure what side the AE86 starter is on, but I would have thought you'd be cutting the primaries at one stage if you used it for RWD (I could be wrong since I saw this on a TA22).
When I tried a set on my FWD everything went together nicely except the bolt on the distributor side. Cut a notch in that hole and you're done. As for clearing the starter, yeah, just move it over or, again, cut the primaries near the head flange and extend them a bit.
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