Since it's hard to get the clutch lined up exactly with the pilot hole even with an old input shaft, if I run into resistance in that last half inch I have somebody disengage the clutch so the disc can slip around a little. That usually does the trick.
It's also possible to leave the pressure plate bolts a little loose, and torque them after the transmission is installed. That lets the clutch disc self-align and makes it a one man job. Sliding the trans in on a couple of long headless bolts is also a good idea.
Jerry