A few things can cause this... Did you press the pilot bushing in deep enough? Are you sure that the bearing collar on the front of the trans is the same size as the hole in the bell housing?
In some cases, once you get the trans as far in as you have, you can put the trans IN GEAR. Get a pal to wiggle the trans while you try to spin the output shaft either with the drive shaft or a spare yoke. I've had situations where I have messed with something for an hour and one simple move puts me where I wanted to be. Good Luck and welcome to the site!