Just an update for those of you who were gracious enough to spend the time helping me figure out what has been going on with my engine.
So far, I have:
Put clean fuel in and changed all the filters.
Oil and oil filter changed several times with 20% marvel mystery oil added during the last one.
Added a Racor primary filter.
Removed the clogged screen at the bottom of the pickup tube.
Replaced the fuel injectors (at 60 bucks each, much easier than cleaning the old ones!)
Compression test: Compression is spot on!
Intake: Filter replaced and entire manifold removed and inspected for obstructions. - None found!
Exhaust: Riser and elbow removed and inspected for obstructions - none found!
Ran about 15 hours at maximum rpm so far.
So....
Everything SEEMS okay with this engine, yet I was still running at only 2600rpms max in neutral vs. 3200 rpms as per the manual while adjust throttle at the engine itself.
So....
She gets plenty of air.
She gets a clear path for exhaust.
She gets clean fuel.
She's got good compression.
So....
I decided to just up the maximum throttle setting on the engine to about 3100 rpm (verified with a "photosensor" tach.).
She runs great at the new maximum speed, and the governor keeps it going at that number when in gear too.
So....
I still get black soot on the transom, yet I don't SEE much smoke at the exhaust at all. I've noticed that bubbles that form along the transom when under power seem to kinda stick to the hull when motoring along rather than dispersing with my wake. Perhaps exhaust debris just tends clings there and sticks to the hull's wax. (I use fleetwax for those who have been following a related thread.)
I still think the amount of air coming out of the breather tube seems high, and if I don't pipe it directly into the air intake, the cabin will stink up within a few minutes. However, since the compression is excellent, its probably not an issue.
I think the low rpm stalling is much better. I've been keeping it at 1000 rpms and it seems to work nicely there, though it might be a little high. I'm sure that the clogged screen on the pickup tube was killing me here. Also, I may have been lugging the engine into a stall by throwing it back into gear when the boat was still moving too fast when slowing down before entering my slip.
So...
I think I'm pretty happy with the way the engine performs now. I'm just wondering why the maximum throttle screw needed to be changed. Judging from the paint on the screw, it looks like it was never reduced by a previous owner.
Hopefully with good maintenance, this engine will last me until the next boat (Benneteau first 30 anyone?).
I sure have learned a boatload about diesels in the process though!