I just did a swap from a 65 coronet with the poly to a new magnum 360. Indeed there is one bolt hole, on the driverside that does not line up. We left it out.
The transmission is different in other ways, so you have to keep your old torque converter as well.
So the problem then be comes balance. The newer engines I thought were all cast crank, the 65 is a steel. So you may have some issues there. The mangnum has a flex plate that is balanced for the engine, so I didn't have to do anything else.

The motor mounts might be different, but the ears should still be there on the newer motor so you can use your old motor mounts.

I like the old poly's, but I wanted efi, so this was a better road to take.

The polys can be bored out 60 over or more according to some sites. Depends on what the sonic test shows.
That guy mentioned above sells a stroker kit for the poly to put out some crazy horse power.