Stovens; There are only a couple things I can think of that would cause that problem.
One is the alinement like you said and you should have a cheap alinement tool for that!
The other is what was behind the 460 before, if it was a stick shift look in the back of the crank and make sure there is not a race in there.
This would keep it from slidding all the way in. Hope this helps Kurt