@Jtullis13 To me, running out of fuel points to a couple of potential resulting problems;
- Loss of prime
- Dirt/debris moving into the fuel filter and beyond
- New fuel filter is a good starting point (preferably filled with SeaFoam to start with)
- The potential for debris to move into the pump and injectors, causing damage
- Actual damage to the pump and injectors from dry running
Since you wrote that your machine has starting / running issues after running out of fuel, I would be inclined to think that all of your issues are caused by running out of fuel. Can you elaborate on what you did to show injector #3 is working? (Pressure test? Spray patter test? Fuel to the injector/hard line?)
What does the inside of your tank look like? Photo? If you can see anything, I would stop and clean the tank before going any farther. If you have rust patches that don't come out, I recommend Por 15's fuel tank liner, with a heads up to carefully follow all of the instructions. When done properly, it is an amazing fix.
If you haven't yet changed the fuel filter, I would do so as a next step, and I would fill it with SeaFoam, ideally running SeaFoam into the fuel pump until the engine is primed and running, e.g. using a fuel line into a one gallon container of SeaFoam.
Good luck, and please keep us posted.
All the best,
Peter