I'll be pulling our engine this year, its approaching 4,000 hrs. I intended to do it last year but opted to leave the boat in the water and do as much winter sailing as possible...we all know how well that worked out around these parts (most snowfall EVER, geeezz).
I did replace the engine mounts this past Spring along with most of the drive-train aft of the transmission.
I have spoken with many people what to do...mostly diesel mechanics and experienced boaters. I get the two schools of thought...1. Its a diesel, it will last forever, do a rebuild and you'll be good. 2. If you're going to pull it, a rebuild will be costly and you still have an old engine thats heavier and not as efficient, so just replace it.
I have recently had the injectors & injector pump rebuilt, but that didn't do much for its starting problems and fuel consumption. That said, I've decided to go ahead and do a "mini rebuild" as you are thinking keeping mindful not to spend to much $$ on it. Buying a new engine is just not in the cards these days, so the choice was easy
At the very least, I will increase my familiarity with diesels and feel more comfortable working on the it or the next engine/boat
FWIW, if I was going to replace the engine, I would seriously consider a diesel-electric hybrid, a diesel generator powering an electric drive, the benefits of this kind of set up seem to be significant, one reason for not just dropping in a new engine as well...waiting to see if the electric drive technology really takes off? Plenty of power for all you needs, alignment issues would be easier to resolve or non existent?, can put the generator anywhere, although it would be in the same general area the current engine is, quieter operation since most generators can be enclosed in their own sound proof box, and there is more but I cant think of it a the moment.