The crank hole does line up with the engine, the e
Start by making sure your crank guide is centered on the cross member. There are pegs on the crank guide that should drop into holes in the cross member for alignment. If the crank guide is not centered, loosen up the U-bolts and repostion it to the proper location. If that is not the problem, check your motor mounts. The front motor mount should have a stud coming out in the center, make sure it is in the middle. The rear motor mounts would have to have some pretty good wear for this to happen as well.