Another thing I have had happen that causes this,
If you have a fuel line that is collapsing, it will do so when the fuel coming from the return line warms the fuel in the system and softens the lines, when the lines are cold they are stiff and the fuel flows freely, do you "hear" any difference in the fuel pump if you shut the tractor off and turn the key to let the glow plugs warm after the tractor acts up?