I fixed the link for your picture in the original post with the new link you sent.

Look at the Yanmar 2GM Operations manual page 12 and 16 at this link.

First - there is a separate cable used for fuel cutoff to stop the engine. The engine should not stop using the throttle control.

Next - if you are unable to reduce the idle using the adjustment, you may have an injector problem (e.g. injector nozzle plugged so it runs very rough and dies).

You may want to pull the injectors and take the injectors to Torrenson marine (since you are in Chicago) to be pop tested, nozzles replace and shimmed. Once they are replaced, you should have an easier time adjusting the idle. It will probably run you ~ $100 if you take them to them. Make sure you ask them for a set of new insulators to replace when you put them back in the engine.