How old is "old", LOL.
You ask what to do about it, there are two answers IMHO. The first answer is to say the "proper" thing to do is remove the injection pump and send it off to be rebuilt and have the fuel
flows readjusted. Now you will also need to replace the injectors as your old ones will not meter the fuel exactly how the manufacturer designed it, and if you are paying for a rebuild
might as well pay a little more for it to run properly. Now you also need to have the rebuilt pump installed and properly timed on the engine. White smoke on startup can also be a sign of poor compression
so you should also at least have a compression
test done and possibly a top-end rebuild
(re-ring and have valves reground)
The fact is that your engine appears to be running reliably and just had some neglected maintenance
that you have taken care of, the issues you have mentioned might affect performance but it does not sound like anything there would affect reliability
, maybe the best approach is to just spend a bit more time on your boat instead of spending it working to pay for engine work, with the exception of having the injection pump timing checked/adjusted.
Now the soot stuff, et al:
I suspect that flakey soot was from your engine simply getting a good and long workout, and this is probably some old soot that has been jarred loose from that. Quite possibly the engine has finally had time to heat up to operating temperature and run long enough to give everything a good heat soak which helps in knocking junk like this loose. The white smoke is unburned fuel (primary culprits are poor compression, too cold engine often from no or stuck open thermostat, or retarded injection pump timing) and black smoke is from a too rich mixture where there is simply too much fuel in the otherwise properly operating cylinder.
Anyway, about the only thing I would suggest doing is replacing the thermostat if it has one, and if the process for checking the injection pump timing is simple do that too but otherwise just enjoy the rest of the season.