If the disc is able to pull back from the flywheel with the trans installed on the bellhousing, splines shouldn't be an issue. It's more likely a problem with the distance the throwout bearing is able to push the clutch fingers. Is there a hole anywhere in the bottom of the bellhousing where you can see the pressure plate operate when the clutch pedal is depressed? If not, it might be necessary to make one (Hole saw, etc.) so you can get a feeler gauge between the pressure plate and the clutch disc while someone holds the pedal down. Putting an inspection hole there won't create any strength issues, and it will allow you to observe the clutch/pressure plate/flywheel relationship with everything assembled.
Jerry
