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Did you clear the code? You can do it with your scantool or just disconect the negative battery terminal for a few minutes and that shouold clear the codes.
The most common cause of a P0401 is the DPFE sensor. It tells the truck's PCM how much EGR flow there is. The die regularly enough that Ford has updated them and tells us that if we see a P0401 to just replace the sensor and dont even check anything else. Any dealer should have lots of them in stock.
Less likely is the EGR ports in the intake manifold are plugged but 99% of the time a new DPFE fixes it.