How much starting fluid did you use? If you sprayed a lot down the intake, there's a good chance things are broken.
If you only gave it a tiny whiff, and nothing was damaged, all that has happened is your tractor ran out of fuel, nothing is damaged or wrecked. You have bled the system; were there bubbles coming out, or just a steady stream of fuel? Bleed it at each port, as in Bill's instructions, until pure, clean, non-bubbly fuel is coming through.
Once that is all through, advance the throttle to full power, loosen the injector hard lines (You don't need to take them off, plus, sometimes they get mixed up for sequence) and crank the engine. Make sure all three lines are moving fuel in equal quantities, without bubbles. It may take a good amount of cranking (up to 30 seconds, in my experience) to purge all the air.
A volt or ammeter will tell you if the glow plugs are working, without having to pull them. Make sure they have some current. The couple tractors I've got with glow plugs get warm enough to determine functionality just by touch, so that may be an option. It's improbable that all three glow plugs failed just because you ran out of fuel.
Get a battery booster or your vehicle, and fully charge your battery on the tractor. Pull the cables off and clean the terminals on the cables and battery well, and make sure the starter motor's wiring looks snug. While it's charging, and you're working on it, leave the thing out in the sun, with the hood up, to get the engine nice and warm before trying anything. Run the glow plugs for 30 to 45 seconds, and with the battery booster/jumper cables attached, attempt to start the engine.
With the additional amperage of the helper power source (whether jumper cables or a charger on "start") the engine should turn over very quickly. You should see smoke, at the least, but I'll be surprised if it doesn't fire within a few turns.
If you can't even get smoke, something is wrong. You'll know if the tractor has reasonably close compression by listening to it. If it sounds about like normal, then there is sufficient compression to at least cause smoke. If it doesn't smoke, it is possible that there is damage to the injectors, but a simple, one-time running out of fuel shouldn't harm them.
Good luck!