Your probably not going to like my answer, but there is a chance you bent a rod when you tried to start it at first, it might have had fluid on top of the cylinders. There was someone with a different brand tractor that had flipped his, tried to start it afterwards, and he bent a rod. He had pictures of it when it was taken a part and it was bent pretty bad. His also still ran but compression would be down on the cylinder with a bent rod.
I would certainly look at other stuff first though, but I never heard of having anything having to be done to the injectors like you are describing.