When you have you're clutch disc in with alignment tool installed put the pressure plate on and snug the bolts down to where they are just starting to collapse the pressure plate but not so tight that you can't still move the clutch disc by pushing up and down on the alignment tool. Once in this position, move the clutch disc around by moving the alignment tool until it is perfectly centered. You can tell when it's perfect when you can pull the alignment tool out and put it back in with no resistance at all. Now it should be perfect. Leave the alignment tool in and torque the pressure plate bolts all the way down and then re-check. The alignment tool should still freely move in and out of the clutch disc & pilot bearing with no resistance. Now install the tranny and if it doesn't fall into place you may have to align the splines on the input shaft by wiggling a little and then it should fall into place. They call them alignment tools but with gravity pulling down on the disc it usually is sitting a little low if you just slap it in there and tighten your pressure plate down. Hope this helps you guys.