2GM air in fuel lines.
One thing nice about the G series Yanmars, and anything older, you know exactly where you are if you get air in the fuel lines. The engine will not run. Any air is an immediate shut down. When bleeding air from the system, you cannot bleed out the air until after the lift pump, when it is positively pressurized. The ultimate goal is to have air free fuel at the injectors. If air is in the lines between the HP pump and the injectors, it merely compresses and in so doing reduces the pressure below what is required to open the injector valve. To get air free fuel out of the HP pump, you must have air free fuel going into it. The main place to bleed is the 10mm bleed screw that is right on the LP side of the HP pump. We never put fuel into the filter bowls. We change the filter, open the last bleed screw available and operate the fuel lift pump. Sometimes the internal lift pump lever is on the high of its actuating cam so you cannot stroke it. This is overcome by rotating the engine a few degrees so that a full stroke is felt. When clear fuel flows at the bleeded, it is shut down, the injector tube nuts are cracked, the throttle is opened and the engine is cranked until fuel drips from the injector nuts. Tighten the injector nuts and start the engine. If your lift pump diaphragm were ruptured you would be filling the crankcase with diesel fuel. The best check is your dip stick. The pumper bulb in the fuel line is for those who don't understand how things are supposed to work and they introduce a number of additional joints that may become air leaks. The 2GM20 governor shoul be set to limit the max RPM to 3600. This is with a wide open throttle, in neutral (don't do it for long). Your 3800 should not happen. It could be a tach problem or the max RPM limiter could be maladjusted. Your max sustained RPM should be about 2900, or less.