I've just fitted a jap spec disc brake diff (early series) to my AE86, but there seems to be a clearance problem at the support between the tailshaft and halfshaft.
Yes ... if you have ever seen the two piece drive shaft on a Jap spec AE86, you'd notice straightaway how much beefier the drive shaft is & the different lengths (not sure which one is longer though) ... same goes for the rear diff for that matter.
I got around my problem by getting a custom made 1 piece drive shaft which has worked fine thus far.
I have seen others adapt the existing two piece shaft to the car but I'm not sure how it was exactly done - you could ask Simon RX7 to have a look under his car for that matter ...