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Considering what you have already done I think you have answered the question yourself. If it was me I would replace the fuel filter (if not already done), I would run a can of a good fuel injector cleaner thru it ( I like both Lucas and Cyclo). I would also consider checking to see if there are any stored error codes, Autozone and some others will do that for free. Just my opinion, maybe some of the transmission experts will differ. Good luck with it.
I doubt it's the trans, but anything is possible. Except Autozone being able to read Ford trans codes. That's not possible.
You might have torque converter shudder. A complete fluid change can often fix that. Here's how to do it yourself. One update, MERCON V is now the right fluid. MERCON has been discontinued. https://www.ford-trucks.com/article/...nsmission.html
On my V10 I replaced all of the plugs and COPs, and still had a miss. I had a bad new COP.