Sometimes you can get someone to push the clutch pedal in while you wiggle the trans and push it in. I've also had better luck using a stock input shaft, than one of those plastic alignment tools for the clutch disc.
That's what I needed to do on my tranny. But it was less than an inch from mating up with the bell housing (just needed to get the pilot bushing lined up.) With the distance on yours, Doug, it sure sounds like the splines aren't engaging. It might be a long shot, but did you make sure that the number of splines on the clutch disk match the tranny input shaft? Might be worth checking, since you're pulling the tranny back out.
