Dropping in motor. Lining up input shaft with pilot bearing?

[AHarada]

I'm dropping in my motor right now. I can't get the input shaft of the tranny to slide into the pilot bearing. I have the motor mounts off the engine to allow more room for moving the motor around. I have the clutch attached to the engine and the downpipe also. How far should I jack up the tranny? Should I take the clutch off the motor and put it in the tranny and use the peek hole to bolt it up to the flywheel? Do I need to press the clutch in or something? I can't figure out what I'm missing.