If the bushing is flush, it's in far enough. Follow Tony's advice, that last 1/4 to 1/2" is most always an alignment problem.
When I was young, I would put in 3 speeds by simply bench pressing them, hold it up with one hand and use the other hand on the tail to turn the shaft and align. After sliding in hold the tailshaft up and put in the bolts. I can't recommend doing that with a sm420 though.
