According to the parts list for 87-90 there is no difference in starters for manual or automatic. The only difference is by year. 87 has different part numbers for the starter and flexplate versus 88-90. 87 shares part numbers with 82-86 CJ7s, which is the starter style with the separate solenoid.
87: J3232138 flexplate, JR775001 starter
88-90: 33004359 flexplate, JR775123 starter
Since you are supposedly not dealing with any 87 parts, this may not apply to your problem but it is possible you have the wrong flexplate, or somehow the wrong flexplate/starter combination.