This is not an uncommon problem with marine diesels. There are several steps to proper diagnosis:

i. Did it ever run properly AFTER the work on the injector pump & replacement injector? If not, it is possible that the injector timing is wrong. e.g. timing off by 1 gear tooth or similar.

ii. The black smoke suggests the engine is overloaded and/or getting too much fuel. What happens to the engine temperature at the point when it bogs down & dies? Could it be overheating due to overload? Is the correct nozzle installed on the injector?

iii. Bogging down & dying under load can also be caused by fuel starvation, although this is not normally accompanied by black smoke. Try running the engine on fuel from a jerry jug, thereby eliminating fuel line blockages. Also check the lift pump for proper operation.

If you still have no luck, I'd recommend getting a certified Yanmar dealer to work with it. Plenty of them in the Annapolis area, otherwise you could come over to see my colleagues at Oxford Boatyard. We're a Yanmar Gold Dealer. (410) 226 5101 M-F 8:00-4:30