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If you still have a vibration at speed ( where you said it had vibration and a dead miss at highway speed), start simple. check all your universal joints. My 2002 excursion with 125k miles on it started vibrating slightly at highway speed with no clunks, codes, or other syptoms ( coincidently right after a cps change that I suspected was the culprit). A trip to Las vegas from Iowa and back pulling a cargo trailer revealed a slight cracking noise on occasion from the reamost u joint. Turns out the needles were all powdered and it was ever so slightly out of balance but new joints fixed her right up. 130some k right now and driving great again. The age of your truck does play into things like condesate corrosion inside of "permanently lubed" universals. If they are originals it might pay to check them.
There is a procedure for cleaning the ebpv valve, although I have never done either of my 7.3's( maybe my lead foot has something to do with that, seems worse after the dp tuner on the f350) but it is considered general maintenance by many.
You mentioned that the EBPV tube was black inside. Did you have a chance to pull that off and clean it out? It can get blocked up with soot and even get pin holes in some cases. I cleaned mine out with a cordless drill, a can of brake clean, and some weed whacker line (the hexagon shaped stuff). Fish the line through the tube and hook it to the drill. Spray some brake clean down the tube and spin the drill. Be careful not to pull it out too far or you'll spray yourself with sooty goo. After a little of that, spray some air through it and repeat the process again.
Don't try cleaning the sensor if its dirty. IIRC, they break easily.