What you're describing is unusual. Yes, tractors slow down and die often enough, but that usually involves certain symptoms. Fuel supply related issues being the most common, but electrical problems usually come in a close second. In many cases the engine won't start, as is your case. Big difference is in most all cases the injection pump will not deliver fuel. With supply problems it's because there is no fuel in the pump. Electrical issues usually involve no 12V power to turn the pump on. In all cases there is no fuel present at the injector when you crack lines and crank the engine over. You say it has fuel squirting at the injectors. Yet it won't run. Any smoke out he stack while cranking?
Timing. That's a possibility with that pump. I expect it's a VE style lock timed pump so the gear on the drive shaft has no key, it's just a tapered, tight fit. They have been known to slip. I'm really not sure how to check timing on that engine. That style pump requires some specific adapters and a certain style dial indicator mounted into the back of the pump. Then certain dimensions measured at a specific point of crankshaft rotation (usually involving timing marks on the flywheel)