I've checked the tune and there is nothing in it that affects CAT, EVAP, or EGR, so if the system monitors are not clearing then there is actually a problem with the systems or you simply have not completed a proper drive cycle to reset all the monitors.
Please be sure to read this FAQ on the proper conditions for system monitor reset. It may help.
Power Hungry Performance Forum - FAQ: Ford F150 FAQs
You probably won't have access to the necessary scan-tool, but just do the best you can. The critical conditions are fuel level and engine temp. They must be followed pretty strictly or you're going to end up fighting the monitors.
Let me know if there's anything further we can help with.
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Power Hungry Performance - The
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