Re: engine change out
I don't know enough about Yanmar models to comment specifically but, whatever you consider, make sure you have accessibility for the things that you need to get to - oil filter(unless you remote mount), oil drain, impeller (and where the bits go if one breaks up), can you bleed the fuel lines? (unless self bleeding), etc. Think of routine maintenance and also things that are prone to give problems.
Most newer diesels are more compact so make sure you can connect everything - for example, will you need a longer drive shaft? Issues with running the exhaust?
Beta makes nice stuff, the key things are easy to reach from the front of the engine and they will supply custom mounts which MIGHT simplify installation.
If all the important stuff is the same on the new Yanmar, that is probably the easiest route. If not start talking to the other manufacturers and ask a lot of questions.