I think the quarter berth is on the port side, but neither here nor there. Probably finding a boat with a diesel inboard is the best advice, but if you re handy and have money to burn, go for it. You do have to make up motor bearers (someone called them stringers before) to fit the foot print of the engine you pick. So....pick the engine first, and then measure twice and build the motor bearers. White oak is a good wood choice as it is strong enough to tap threads into it for your motor mount bolts. But, white oak will also warp with weather, so you want to seal it up well or encapsulate it with fiberglass. You have to fiberglass it with roving anyway to make sure it is a very strong base for your engne. You need to run the shaft through the hull and so you need to figure the angle of the shaft from the engine to do that. The easiest way is to make a large hole for the shaft log and put your motor on the mounts on the bearers, connect and run the shaft through and then put the shaft log fiberglass tube (you can buy them made up) over the shaft and figure the lining up of that. Then when you know all components will work, have clearance, etc., you can fiberglass the shaft log into the hull with the engine pretty darned straight as you want it. You will need a cutlass bearing and the stuffing box (which attaches to the shaft log with a rubber hose and clamps and you also might need a strut (bronze with a cutlass bearing) to support he shaft outside the hull. Consider the right prop so you have the required hull clearance, which all will have to factor in to the angle of the inboard. So, there is some contemplation here.
You have to install the wiring harness which usually comes along with a new engine as well as the panel where you find the ignition and gauges and lights, etc. You also have to install a diesel fuel tank and you will have to consider that it has fuel lines to the engine and fuel return lines back to the engine. You have to measure the space beneath the cockpit where the engine will go and then make sure you get one to fit. And....you have to be able to find the dip stick, be able to pack the stuffing box packing, put antifreeze in the closed portion of the cooling system, install a water separator filter that is accessible, etc. I have done it successfully, but it is a lot of work, but fun for the right person. Do it for your own pleasure because you will never get the price you pay back when you sell the boat. At least an O'Day 25 boat.