When installing the engine with the transmission already in the car, it’s critical that the clutch disk be aligned perfectly with the pilot bearing. This is done during installation of the clutch. I have had very little success with the plastic dohickeys sold by the vendors. Rather, I have an old ****** input shaft that I use for this purpose.
I jack up the rear so one wheel is still on the ground, put the ****** in high, and spin the other rear wheel to rotate the car’s ****** input shaft to line up the splines into the disk. From there it’s a straight push.