How to do a EGR delete on a 2004 f-450 6.0 powerstroke diesel

no ecm wont adjust it will be setting off more codes and stalling the egr can also cause a no start problem need to fix and hook the egr correctly

code p 0401 is the EGR va;ve but the principle reasons for problems are EGR valve
EGR solenoid
hose blockage and wiring
code p 0460 refers tois the fuel tank level sensor--low input===causes ---wiring short to ground --fuel level sensor--ECm

If you have to replace them frequently look for some emission/ dirty exhaust problems.

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there is no wastegate on a 6.0l turbo. its a variable geometry turbocharger and doesn't need it. i have never seen a turbocharger cause a misfire, the turbocharger is most likely not your problem. if you didn't clean the intake out when replacing the egr valve there is a really good chance that the egr is bad again. also, a bad egr cooler can cause repeat egr failure. also, fuel injector control module is a common cause for misfire

if it is a ford 6litre diesel there is a egr delete kit available at the dealer

Sound like this has a turbo?? And this is the culpert!

Check fuel pressure at the rack and at the pump unit.