If you haven't gotten the tranny in yet, pull it out, push it out of the way.Take your alignment tool, you did use one right?, and make sure the tool slides in all the way ,seats completely into the pilot bushing.Now throw away your alignment bolts,useless actually,and using your tranny jack, with the trans in gear, put the tranny back in, carefully,wiggle the output shaft to help the spline find it's way into the clutch disc .It should slide in no problem.The tranny must be perfectly square to the bellhousing,don't worry if it's rotated one way or the other, you can rotate to line up the bolt holes once it's in all the way. Gently rock the trans slightly side to side and up and down while pushing in . Of course this is all complicated by cold weather, too many or too few beers or the tranny jack is on an uneven surface.And like the guy above said,same tranny that was removed from the truck?Not a later 4speed with the larger front retainer?