I don't know how the Yanmar fuel solenoid works but on my Perkins it has a rubber tip and is spring loaded. If you kill the power the spring forces it closed. If you remove it diesel will pour onto the ground. I thought that it has been replaced. If it can be removed without causing a diesel leak then that would be worth pursuing. In the end the idea is to try and eliminate everything but the injection pump $$$$. If you can see fuel in the sight glass then the problem must be closer to the engine.
Looking at a picture of the solenoid it looks like a simple pin that pushes in to shut off the fuel (or pushes in to turn on the flow). This tells me that what ever the solenoid pushes is inside the injection pump could also be broken. I tried doing a search for the solenoid but I found two that look like it but one had 2 wires while most had 3. If it does just have two then if it has power when it shuts off then it's not a safety interlock. I remember Mike saying he tested it but I don't remember how. I would try to rig up a light to the connector. If the light stays on when it shuts off then it's not an interlock.
With a 3 wire system you need to find out what the 3rd wire does. I would assume if this is the case that two wires would just be the power when the key is on and and ground. The 3rd wire come from the computer. If the key is turned off the relay would cut positive to one of the two wires. If the computer thinks it needs to shut the engine down it would do something with the 3rd wire (put power on it or turn power off). A simple multimeter would be very helpful to identify the wires and what they are doing. My simple test with a light would still work but you would need two, one for each wire.
With a 3 wire system you could buy a cheap aftermarket solenoid (hopefully not expensive) and remove the wire that goes to the computer from the connector. Try starting the engine. With a multimeter you could measure the voltage coming from the computer. If it's 12v then you could simply connect the 3rd wire on the solenoid to the battery and run it to see if it shuts off. If it's 0 volts then the engine should start with the wire disconnected and again you could run it to see if it dies.
I know this all reads like a 4" thick novel but that has been done is early posts. (#17)
"UPDATE> Ok, my test lights are complete and here are the results:
The white solenoid lead is the startup power. It does in fact come on with the starter and then go out. The red lead is the hold, and it also comes on when is running and stays on.
So, I finished cutting the grass this morning and was out of work for "overheat testing" so I started in and sat in my yard watching for the light bulb to go out when the engine died. Sure enough 30 minutes later it died and behold the light stayed lit until turning the ignition switch off. So my take is it's not the shut off solenoid but somewhere else, although if I had not just replaced it I would have suspected it to be bad."
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