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I would start with checking the fuel pressure. Sometimes you will get a code for the fuel rail pressure sensor when the fuel pressure is low. This is going to cause rough running and misfires. Especially under load, but with low fuel pressure it would be consistent. On the 4.6 you usually have to tie into the fuel line where it comes to the rail due to the lack of a shrader valve for testing. Start there and also check for intake manifold leaks. Again though with the fuel rail sensor code, it's more then likely low fuel pressure causing the problem.
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Well you would have to maybe rent or borrow a fuel pressure tester. Harbor Freight actually sells them fairly cheap or you could possibly pay a shop to check the pressure. Without the proper tools it's going to be difficult to properly diagnose the truck. Since you don't have any misfire codes, that indicates the coils and plugs aren't the issue. As for testing for intake leaks, with the engine running spray some carb cleaner along the intake manifold and vacuum lines. If the idle speed picks up or smooths out, that indicates a leak.