Well, first off, the Atomic 4 is a gasoline engine not a diesel. But I have to ask, have you though about rebuilding it instead of replacing it?
The A4 is an incredibly reliable engine, easy to work on, parts are still available (moyermarine.com), low fuel consumption, quiet, etc.
But getting to your question on how to remove it. If you can get someone to cut out an opening and then redo it, that would probably be you easiest option, although probably not your cheapest.
My friend has a S2 center cockpit with an A4 in it and we removed it by taking the engine apart where it sat and took it out piece by piece. After we got it down to just the block, we used a couple rachet straps to attatch two lengths of pipe on top of the block, and mahandled it through the opening in the cabinates.