Paul,
If the manual, or in the case of your Yanmar there is a plate on the engine, states that WOT is 3,600 RPM then what is the question.
That engine was meant to run at 3,600 top end for short periods of time and at 80% of 3,600 which is 2,880 day in and day out. There are several things that enter the problem at this point. 1. Is the tach reading correctly (check it with and optical tach) 2. If it is then, in gear under way the engine should reach 3,600. If it doesn't the pitch or the prop or size of the prop is not correct. To much pitch or to big of prop will not allow the engine to get up to speed. The prop in essence can act as a brake. Nothing beats an adjustable prop because the pitch can be changed on most while the boat is in the water. All of the pre calculations for the most part will only get you close. Which may be just fine. The final pitch is usually set after the boat is in the water and it is tested. Once the engine can reach 3,600 at full throttle you are there, then run the engine at 2,800 and all will be well. Your engine will be happy your fuel burn will be where it is suppose to be and the engine will live a long life.:dance:
Hope this helps. Any prop information (size, pitch) can be obtained from
http://boatdiesel.com/
The real experts are there. If you really want to know about your engine and what is the correct thing to do this is the place. There are real experts on there for every brand of engine.
Good luck