If your tractor ran before you ran out of fuel, which I'm assuming is how you ran out of fuel, then I would think that everything is fine with your tractor. I know it's real easy to look for other reasons for something that's not working, but with air in fuel lines, it's just about being patient and sticking to it.
I don't know of any electrical fuel injector pumps, but don't know enough about diesels, modern autos/trucks or the high tech stuff to know if they exist or not. On the tractors that I have, and I'm assuming yours, is that the injector pump is timed from the flywheel or camshaft. Having it timed (connected) to the gears makes sure it works at the right time, every time. Simple and effective.
Did you take off the fuel line before the injector pump? I've gotten impatient and tried to take a shortcut on mine. I've even had fuel at the injectors, but couldn't get it to start. Sometimes you will see fuel, but there's still air in the lines. You also need to loosen all the fuel lines from the injector. Sometimes one or two of them will get the most fuel and if you pulled the week one, it might not bleed out the air. If it doesn't bleed out the first time, you just have to do it again and again until you get it right.
Did you pull the fuel filter and make sure it's full of fuel? This was my mistake the last time I ran out of fuel. I wasted an entire morning trying to get my dozer started, and then went and bought five gallons of diesel, filled up both fuel filters and had it running in about half an hour.
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Today's Featured Article - Third Brush Generators - by Chris Pratt. While I love straightening sheet metal, cleaning, and painting old tractors, I use every excuse to avoid working on the on the electrics. I find the whole process sheer mystery. I have picked up and attempted to read every auto and farm electrics book with no improvement in the situation. They all seem to start with a chapter entitled "Theory of Electricity". After a few paragraphs I usually close the book and go back to banging out dents. A good friend and I were recently discussing our tractor electrical systems when he stated "I figure it all comes back to applying Ohms Law". At this point
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