Originally Posted by SecondWindNC
I think you may be jumping the gun with completely rebuilding a running Yanmar at 3,300 hours. The life expectancy of a well-maintained marine diesel can be well upwards of 5,000 hours (sometimes more like 8k-10k). Have you had problems with the engine that have led you to this?
I would suggest doing an engine survey instead. Have the compression tested, injectors tested, etc. Fluid (oil and coolant) samples can also reveal a lot about the engine. I'm sure there are some mechanics in your area that do engine surveys. Address any problems that the survey identifies, and go on enjoying your boat.
The Life Expectancy of the Marine Engine - BoatSafe.com
I agree with the above. Check the fuel injection pump. Most likely there is nothing wrong with it, but water in the fuel can cause premature wear. I would also replace the injectors or at least have them reconditioned as a poor spray pattern can cause premature cylinder wear. At the very least have the injectors tested. Of course have all pump impellers replaced. I would also do seals on any water pumps. If there is engine oil in the bilge, check front and rear crankshaft seals. Maybe oil is from poor technique with oil changes is the cause. Crankshaft seal replacement requires pulling the engine. . If this were direct cooled, no heat exchanger, I would disassemble and test for cracks and corrosion. If there is a heat exchanger, have that cleaned out of corrosion products and scale. If compression is not all right, pull the head. Maybe all you need is a valve job. The cylinder walls can also be measured and inspected for wear with the head off. If you have bearing material in the oil, pull the engine. You will probably need to have the crankshaft ground and certainly new bearings including camshaft, mains, and rods. You may be able to use the old pistons with new rings with cylinder glaze broken or honed. Diesel cylinders usually wear little because the diesel is light oil and does a good job of protecting the cylinders. If the engine has had seawater flood back into the cylinders because of excess cranking or poor cooling system design, a compression check should tell the story. Also check the cutless bearing on the propeller shaft for wear. Take the flange loose from the transmission, put a very short bolt between the flange on the transmission and the propeller shaft on the other flange, put the bolts back on and tighten to push the propeller shaft out of the flange attached to the propeller shaft. Do not use a slide hammer as this can damage the transmisison. Slide the propeller shaft out to see if there is any pit corrosion on the shaft. Stainless 316 and 304 steel is a poor choice for a propeller shaft. Consider 22 alloy: Western Branch Metals: Marine Propeller Shafting
Also send the propeller out to have a computer analysis done to check for damage and get the shape and balance accurate.