If the clutch disc wasn't aligned properly the input shaft won't align with the pilot bearing. Have somebody push the clutch peddle in while you try and wiggle and jiggle the tranny in the last 1/2 inch. "DO NOT" try and tighten the tranny bolts to draw the tranny in.
I also ran into this situation installing my SM420. Sometimes the plastic clutch alignment tools are a bit off. 55shaker's advice is right on the mark. I had my wife push the clutch in while was pushing with my feet from below. The transmission went right into place. I also obtained an old input shaft to use as a clutch alignment tool.
Good luck,
