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Hello, When you have black smoke coming out of the exhaust is it running rough?
If the EGR is new and not sticking open anymore then you have a fuel injector problem. Ford scan tool offers an enhanced power balance that will show if a cylinder is overfueling or sticking open. That is what I would do to diagnose this vehicle the quickest.
There is one called blue driver which seems to be one of the better ones. This is the one I would go with. If you have other questions please let me know. Also please remember to rate my answer so I receive credit for assisting you.