Pictures would help, but I can say from experience since I completed a similar swap a few months ago with a 383, you want to get the drivers-side in first then do the passenger side which is a royal PITA and will fight you a bit going in. I did, however, use some aftermarket copies of the Schumacher big block motor mount plates and not NOS parts. This could have been why.
My advice would be to use a good pry bar to manipulate the rubber isolater a bit to get her in. Once I did that mine dropped in. There are alignment pins on the motor mounts that fit into the K member so that is probably what is hanging up and causing your issue.
Also, depending on how you are supporting the engine with the crane it may not be completely level and causing this issue as well.