[Batman]

Aftermarket pressure plates will not always be the same height as OEM or other aftermarket pressure plates. Turn the flywheel and there you introduced another variable. This is not a Pontiac specific problem.

You need an adjustable pivot ball http://www.summitracing.com/parts/sum-700110 and/or a longer throw out bearing. There are several lengths available, but measure your old one and order one 1/4 longer to start with. There is also a longer clutch pushrod available from GM- I think it is a Corvette p/n but will fit or you can do what I've done in the past and weld an acorn type lug nut that fits the clutch fork recess if you need a longer push rod length.

FWIW I never use the clutch disk alignment tools anymore as they just aren't worth the trouble. With the pressure plate bolts started enough to hold it in place but still allow moving the disk, get a straight view at the disk with a good shop light head on and adjust the disk to dead center using a ratchet extension or something similar in the pilot bushing. Using your dominant eye it's pretty easy to center the pilot bushing hole in the clutch disk hole and then tighten. If it's off a bit, as others have said have someone push in the clutch pedal while jiggling the trans in from underneath, but honestly this is rarely required.

Also, it's not real intuitive but sometimes you have to push straight up slightly on the front of the trans to get it to pop in even though everything else looks perfectly aligned. You will probably be very good at removing and replacing your trans when you get done. Just my experience.

I've also learned the hard way over the years to ensure that pilot bushing/bearing fits and the clutch disk slides freely all the way on the trans input shaft and the clutch disk seats on the installed flywheel before trying to assemble anything. Yes, clutch disks can bottom out on flywheel bolts