Be aware that many modern engines have head bolts that are designed to be tightened to the point where the bold stretches (elastic deformation) to the point that if you remove the bolt and compare it with a new bolt, the old bolt is longer. In other words, if you need to tighten the head bolts, you will need a new set. I do not know if this is true for Yanmar engines. If you are going to replace the valve cover gasket, consider this product: Permatex Hylomar Universal Blue Racing Formula Gasket Dressing & Flange Sealant available at your local automotive parts store.
Yanmar Manual (operation manual, does not include major engine work, click on page number in table of contents for that page of the manual)
1GM10-3HM35 SERVICE MANUAL (about $95, but necessary if you do any engine work, find it with Google)
I have been disappointed with Clymer manuals for automobiles and trucks. Maybe the boat engine manual would be better, but do not buy without inspection first. Usually these books have little information on a particular engine and pad books with very generic descriptions on maintenance.
For general information about diesels: Marine Diesel Engines: Maintenance: Troubleshooting, and Repair by Nigel Calder
For a simpler book for general information on diesels: Troubleshooting Marine Diesels by Peter Compton