If it's accumulations of soot, then I would also suspect the mixing elbow - that can accumulate carbon and restrict the elbow. You can remove the piece, soak it in oxalic acid, clean and stick it right back on (they can be a bear to remove).
Just running the motor at a fast idle to charge batteries is really, really tough on a diesel. They need to be under load. Using the motor to charge to batteries or chronically under-revving it (lots of people cruise at 1500 or 1600 RPM thinking they're going easy on the motor) can cause a condition called "wet stacking" that will accumulate unburnt fuel components on the exhaust side of the motor and on the cylinder walls. It will eventually damage a motor and shorten its life.
If that is really your only way to charge the batteries, try putting the boat in gear when possible.
