I recently bought a 2007 Expedition with just under 100k. Not long after I got it I started to experience shuddering during acceleration as well. On one occasion I also saw the CEL come on, then go off shortly after. Took it to a mechanic right after the CEL and found that no codes had been stored. His next question was whether the plugs were original, which they were. Said it was very likely a bad plug or plugs (possibly a coil pack) and that a brief misfire (hesitation/stuttering) did not always cause a code to be logged. A second mechanic made exactly the same diagnosis, with no prompting from me. After changing the plugs and coils packs, the problem disappeared. Stress tested by towing 3600# across the Sierra Nevadas and Great Basin.
This doesn't explain the fact that your problem goes away with the overdrive off, but perhaps a contributing factor? Unfortunately I don't remember if having the O/D on or accelerating at a particular RPM made a difference.