I'm not sure if it's the exact same setup as the Super Duty trucsk, but if that F550 has the 6.0, and you want to get away from the EGR problems, it's real simple. Buy an SCT XCAL 2, from either Diesel Innovations, Elite Diesel or Spartan Diesel, and they all should have a custom tune, or could come up with one specifically for your F550 that can turn off the EGR function. The tuner can even make your engine perform better, and they can even function the VG turbo like an exhaust brake to help save wear and tear on the rotors and transmission.
From researching 3 different sites before I bought my SD, the EGR cooler is just as big an issue. The EGR cooler is a pipe that runs from the DRV side up pipe to the bottom of the air intake just below the EGR valve itself. It's a water jacket that has engine coolant running around the pipe directing exhaust to the EGR to cool the HOT gas before it's reintroduced to the engine. The collective assumption is the thin cooler metal goes through one too many heat cycles and splits, which allows the exahust to bubble into the engine coolant, it overpressures the closed system and the coolant spurts out from under the cap on the degas bottle. Turning off the EGR will keep the exhaust out of the intake stream, but you could still end up with a split cooler. Google the Powerstroke EGR delete or bypass kit, and you can eliminate the EGR and cooler all together.
The turbo has been changed a couple of times to try to eliminate the sticking vanes. Either it's from excessive carbon build up, or rust on the vanes and actuator plate. There is a service procedure to remove and clean up the turbo, instead of replacing them all the time now. If you're so inclined, you can pull the turbo and clean it in your garage instead of making a call to the dealer.
The SCT with the custom tunes from one of those vendors is considered the best tuner for the Ford 6.0 right now. The inline or after-ECM modules are real good at wiping out the Torqueshift because they don't rework the shift strategy like the custom SCT tunes do. A pyro and real tranny temp gages are a real good idea if you add the SCT, or even in general. I am going to do all this in the future eventually.