Ford extended the warranty on the DPFE sensor. The EGR is not covered beyond 36K miles.
Some emmission parts are covered under the federal 8 year, 80K mile warranty but the manufacturer determines what parts of their system are covered.
The only way to know is to go to a Ford dealer and have them make the repairs. Their parts department has a list of parts covered under the 8/80K warranty and you can compare that to what they replaced on your vehicle to verify they honored the warranty. If not you can get a refund.
Unfortunately, the OBD-II diagnostic codes do not guarantee that is the part that failed and Ford requires that they do their own diagnostics and follow specific testing proceedures to verify which parts need replacing, so they will not usually guess what the problem is in advance.
...Rich