I have had terribly bad luck with getting the clutch to align even with the tool or even spare input shafts. I usually leave the bolts on the pressure plate loose enough to slide the disk inside the clutch but tight enough to hold it in place if you don't force it to slide. Once it is together I bolt the pressure plate down. Not an option on most racing bell-housings though.
I've had good luck hooking up the clutch linkage and having someone step the the pedal to get the input shaft to align and seat.
