I think crosswind had it right originally. Make sure the fuel control rack is lined up so that the pin fits in the fork of the governor arm shown in the attached diagram (labelled Governor Level 2). I had my injector pump off a few years ago and the manual stressed that the pin needs to fit in that fork or you could have an engine that doesn't shut off. Perhaps the pin is seized as you suggest. If I remember correctly, there is a plate on the timing gear cover just under the injector pump that you can remove to peer inside and verify that the fuel control rack is aligned properly. Once it is fit properly, I don't know how it is possible for it to slip out, so I'd bet there is something else that is a factor, but I'll suggest that the alignment of the fuel control rack is the crux of your problem. There should clearly be a pin that fits in the fork so that the governor arm slides the rack back and forth. If the rack is open and it's not sliding, the engine will run at wide open. The maintenance manual explains it pretty well as I recall. I'm not a mechanic but I was able to remove & reinstall the timing gear case cover and fuel injection pump without much difficultly. What I'm writing could be based on faulty memory, I'm sure. It was a 1-1/2 years ago.
Scroll down in the link to find the diagram.
Yanmar 3GM30 - No Fuel at Injectors 2 and 3 - Cruisers & Sailing Forums
Hi to all from NZ, I have posted in another thread but I think this subject deserves its own heading for those in the same situ later. My motor has been sitting for 7yrs whilst we rebuild our boat .(&a
www.cruisersforum.com
Scroll down in the link to find the diagram.