Need Help - John Deere 997 Mower Inj. Pump

I have a John Deere 997 zero turn with Yanmar diesel in the shop. It would run perfect for about 20 - 30 minutes, then shut off. You turn off the key, switch off the deck, home the speed control levers and park brake. Then crank it maybe 15 - 20 seconds and it would start, but each time it would shut off after shorter use times. Searched the 997 shop service manual and the net, but all I can find is the fuel shut off solenoid is defective, so I ordered one. Had a young helper wanting to work on it because it looks simple to change the solenoid. He pulled the top screw / bolt on the solenoid. Then he took out the other, but the solenoid would not move. I looked at it and he took out another bolt or pump adjuster of some kind right next to the top solenoid mount ear. It is a stud with a long nut and a lock nut. Pump shop manual calls it Maximum Speed Limit Bolt. We put the new solenoid on and it cranks great, but no start. Put the old solenoid back on and no start.

What does this stud with the lock nut do? And is it adjusted on a pump stand? Did something drop out of location? Do we need to bleed the system because the solenoid was changed? O ring is on the solenoid body. Pump is a Yanmar Mono-Plunger. Engine is a Yanmar 3TNV82A.

No experience with that tractor or engine but if the solenoid has an oring that likely means it seals in fuel. When you had it out you introduced air into the system so in my experience with other diesels you now need to bleed the pump and injector lines. Hopefully you can find the steps to that process online. I am pretty sure the Yanmar engine manuals can be found online. Also an operating manual for the mower is available free at the link.
JD publications

The problems I have had with the fuel problems with the Yanmars has been the lines in the tank. Cracked,clamps coming off. I had a gas Agco that would run across the yard and die,wait 10 min and it would make it back where you started and die again. That was a small cocoon that would flush itself out of the 90 deg bend when it died.( I still have a new fuel pump for a 25hp Kohler)

I have an x748 with the yanmar. The fuel shut off solenoid on mine bolts on with 2 bolts, it has a pin or needle that sticks out on the end that goes into the pump. This is spring loaded to push against a plate on the inside of the pump when key switch kills power to the circuit. There is a relay that sends power to the solenoid electromagnet to pull the pin back to allow the machine to run. you can take that solenoid off and start the engine, it will leak oil out of the hole but will let you know if it runs or if you have another problem. If the engine runs with no solenoid then you have a relay problem or an issue with getting power to the solenoid.
It doesnt have any fuel to it so doesnt need bled. If you think its a fuel issue then start with the filter housing connections and work your way back to the tank, low air pressure applied from the supply hose at the filter might help you find any leaks you might have. The relays on these things are a bugger to diagnose, i converted mine to a manual shut off.
As for the long bolt i dont know wht it is or how its adjusted but based on what you said i would say its just a bump stop for the governer to limit rpms, if its out i would have something to put over the air intake if it starts as it might open up without that bolt in place.

Different animal, but, my 1145 was doing that last year. It had dual tanks and lines with a separator valve. Figured the problem had to be something other than the tanks. Ended up being the tiny screens on the end of the suction ins in each tank. Who would figure they would both act up at the same time? Mine was definitely running out of fuel as the filter would fill with air. A quick bleed would gain be another 20 min. Try blowing air back into the tank and see if it clears up. Last picture is my {more permanent} solution.

I have owners manual, John Deere service manual, parts manual, and Yanmar injector pump shop manual. It has new filters and water separator filter. All this before it started acting up. When I got it in, I mowed with it 20 minutes perfect, then quit just like I turned the key off. I would home all the safety switches and try to start it. It cranked 15 - 20 seconds and start like normal. I would mow for maybe 10 minutes and repeat. Then it got down to once across the yard and quit. The shut off solenoid was hot when I checked it. I even got a blister on my hand. Used my ohm meter and it tested bad so I got a new OEM one. I even started it and drove it into the shop. My helper removed the old one along with the maximum speed limiter screw. I put that back in and tried both solenoids but it has never hit on any cylinder since.