I can only speak of the difference between Yanmar 315 LP and Cummins B series factory reman, all in Wasques. When repowering, I chose the Cummins reman over the new Yanmar, and I am happy with my choice. The Cummins does vibrate at idle, but I have solid mounts. The Cummins was cheaper to buy (it is a reman) and super easy to work on (I do all my own engine work), and parts are cheap. There is no turbo whine until over 2500 RPM at 21kts (2800 RPM max). I get 2NMPG at 20 kts.
The Yanmar was smoother at idle (if I recall correctly) but wow, that turbo whine was exhausting for me. I could hear it even at 16-17 kts and it gave me a headache. I don't know the fuel burn difference, but my buddy said the Yanmar (common rail) would be better than my Cummins mechanical B. Since I'm not a high hour/yr user the cost difference wouldn't be worth it for me, assuming there is one. He also had engine electronics issues, something I've never had to worry about.