Did you bleed the air off after having the lines/etc open ? Sometimes you need to turn the bleed screw on the injector pump, allow fuel to flow a bit (you'll see little air bubbles IF you have air in the system), then tighten the screw back down.
If that isn't it, make SURE you're getting a good flow of fuel from the tank to the filter inlet. Unless you completely removed the tank, turned it upside down and flushed it, you can have a small obstruction (has happened TWICE to me, both time it involved insects in the tank) that floats around in the tank, then floats over the fuel outlet point, blocking enough flow to starve the tractor for fuel.
With the tractor sitting level, let it run until you hear it start to die. First, if you have a clear fuel bowl with a little pre-filter, IS THE BOWL FULL OF FUEL ?? If you can see any air space in it with the tractor trying to run, you DO have some obstruction between that bowl and the tank.
The last time it happened to me, I used a Rigid brand inspection camera (Home Depot) to look right in the tank at the outlet point, and there lay a dead wasp right over the 1/4" outlet hole. I took a long set of 'finger-grabber' things, reached in while using the camera, and pulled the dead critter out.
Problem solved.