The thing that has always struck me about marine diesels is that they are soooo expensive.
An idea I fancied trying one day would be to use a secondhand automotive engine.
An engine I like is the VW V6 Tdi. Its a stonking engine, smooth, very torquey and its comparatively short being only 3 pistons long.
The biggest problem as I see it is separating the engine electronics from the car, immobiliser etc.
Things like heat exchangers needn't cost too much, I could never work out why the mercruiser one was £700
Also if you make an engine box, go from tube to tube to give yourself plenty of space to work on the engine.
Hope that helps