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