Yes, there should be two alignment pins (AKA dowel pins) that will have to be aligned to allow the tranny to slide in. What I found to be the most critical was keeping the tranny and the motor in the same plane to get the input shaft to slide in. I used two floor jacks on my XJ to allow me to adjust the fore and aft of the tranny, a tranny jack would have been a real time saver. Also, try putting the tranny in gear and turning the output shaft to relieve binding as the input shaft slides into the pilot bearing. And last, I've always found it easier to get the input shaft to slide into a pilot bushing rather than the newer style pilot bearings, which don't ever seem to last either. Good Luck
Woody