This could be a number of things. First and foremost we need to check the fuel pressure as I suspect you have a regulator issue. Here is a guide that will help with this:
The other possible cause is a leaking injector. So we need the fuel pressure because if you have high pressure then the regulator could be the issue but the pressure may be slightly low and with black smoke would indicate a leaking injector.
There is a strong possibility that the fuel pressure regulator is stuck open causing a rich condition that is giving you the black smoke-rough running condition from extremely high fuel pressure. The fuel pressure regulator is located within the in-tank electric fuel pump assembly. Here is a tutorial showing how to check fuel pressure. The fuel pressure specification for your truck is with key on-engine off is 55-62 PSI.
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