Spec aluminum flywheel and alignment pins HELP!!!

I have a spec aluminum flywheel but ran into a problem when I went to use the stock ford alignment pins for the pressure plate. The alignment pins are larger on one side which is the side that is normally beat into the flywheel. When I went to put them into the spec flywheel only the smaller side of the pin fits into it.. and only the smaller side fits into the pressure plate. Ive been having a vibration problem with this car which I believe is related to the pressure plate not being center... If anyone has run into this problem please let me know how you resolved it.

Well I just found out the vibe isnt in the clutch alignment.. we started the car with the bell housing on and without the pressure plate installed and the vibe is still there.. we have tried two different balancers and even tried removing the belt to make sure it wasnt the fan or anything else the belt is turning causing the vibe... my next step is to bolt a stock flywheel on to at least eliminate the posibility of the flywheel being off balance.. I have the spec stage II pressure plate on my own car and picked up a vibration when it was installed... I then had to tear my motor out for other problems then had my machine shop balance the pressure plate and found out it was way off balanace and spec must not have balanced this pressure plate properly...After that my vibe went away. I had thier stage 3 in befor that and had no problems with it... my stage 2 had the light weight option wich may have had something to do with the vibe as maybe they didnt check for proper balance after drilling the holes... oh well onto the next step.