Small Engine Troubleshooting Problems? Ask a Mechanic Now.
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What you have done up to this point should be all that you would need to do with the exception of adding diesel fuel back to the tank and bleeding the air from the lines and filter in order to get the machine back up and running. It can take a little bit of time to get all of the air out of the lines when you have a situation like this but the easiest way is to remove the line going from the injector pump to the fuel rail or injectors and crank the engine over until you have a steady fuel flow there with no air bubbles coming out, then reconnect the line and you should be able to start the tractor again with a few attempts.