Is the check engine light coming on?
Have you had it checked for codes?
The EGR valve is located on the intake manifold between the alternator and oil filter. It has a electrical plug on the top. I would recommend to remove it and inspect for carbon build up and the valve not being fully closed. It it is carboned up or the valve does not seem to be fully closed then it would need to be replaced. If it looks OK the more diagnosis would need to be done. The next test would be a fuel pressure test.
The diesel warranty is on good for 5 years or 100,00 miles. and 2004 model would be out by time.
The other thing that has me slightly wondering is you said this happened after a fill up. Are you certain it was filled with diesel and not gas? This could also be a symptom of gas in the diesel fuel.
Here are the labor times for replacing the injectors