We're looking at a Mainship 40 with a Yanmar6LY3-UTP. Any problems with that engine that you know of?
The problems with ANY high reving high horsepower to weight engine are the same. The engine life will be 100% based on how the engine was run, and how it was maintained.
Most people don't realize this, but high HP to weight engines, if run at high horsepower settings just do not have the same life as if they were run at low horsepower settings.
So, looking at a semi displacement boat with 2K hours on a high HP-weight engine like the Yanmar, or the Cummins (just two examples) is really a crap shoot. If the engine was run hard it could be much nearer to end of life than you think. If it was run easy then it could have a few thousand hours left in it.
The problem is that at least with the Cummins (I've never had a Yanmar) engines a engine survey is not that great at predicting where in the lifecycle that engine is. All you really get is oil analysis and blowby. Actual under load testing will determine if the engine meets specifications that day only. Remember that they don't take apart engines for a engine survey.
Then you run into maintenance. On these types of engines manitenance is more complex and expensive than other engines. Aftercooler servicing is the really big difference. This can be a pretty expensive job, and maintenance records are the only real way to determining where in the lifecycle the aftercoolers are.
For those that think high hp to weight diesel engines typically last a really long time, just look at Yacht World. Try to find a high HP High reving engine on YW with over 2K hours on it. Its pretty hard. Then try the same thing with lower HP to weight engines. you'll see these with over 5K hours really consistantly.