Engine Lock Down

The convertor should move iinto the trans about 1/4 if its not torqued into the flex plate. Line bored? That would move the crank and centerline up Offset dowels can correct this. remove the dowels and see if it will bolt down. If so, put a plug of clay in the dowel holes and mate em up again. then carefully seperate them and check the clay for any offset between the 2 alignment holes.