I am not familiar with the Atomic 5411, but I believe it is a diesel Engine.
There are 3 things that a diesel needs to run, and any of them can be used to shut down a Diesel engine:
1) Fuel - the most common way to kill the engine is to stop the fuel flow. My Yanmar has a pull knob that stops the fuel flow to the engine…on my Yanmar, that fuel cut-off is at the engine. On newer motors, the key is used to shut off the fuel via a solenoid…so it is electronic, but it does the same function. You may want to follow the fuel cut-off cable down to the engine, and see what lever it actuates. I can kill my engine right at the block my manually moving the lever that the fuel cut-off cable actuates when I pull the know in the cockpit.
2) Air - not real practical, but you could block off the air intake (remove the air filter and stuff something in the intake hole… don’t let it get sucked in, or you will have a real mess. But if you had a ball of some kind, larger than the intake, but close enough to block off the air flow, you could kill the engine. This is a good technique to understand if you ever had a “runaway” engine and no other way to shut it down.
3) Compression - a diesel needs compression. This creates the heat needed to ignite the fuel. Without compression, the engine will not (normally) run. I say not normally, because in a runaway situation, the fuel or engine oil may be burning and create enough heat to “run away” regardless of the compression. On my Yanmar, I have decompression levers, that I can flip that relieves some of the compression pressure in the cylinders. I don’t think engine manufacturers recommend stalling an engine using the decompression levers, but it could work if you have them.
Good luck. I assume your season is about over up there in Milwaukee. I am waiting to the last day my marina will haul out, October 29 this year. I hope it is not snowing when I haul out!
Greg