If you're still having the problem at stock, then it's not the tune. I notice you have a CAI on your truck. What year is the truck? I'm guessing it's not a new model. CAIs on the 04-05 trucks especially can cause the engine to run lean.
Are the throttle body and MAF sensor clean?
And, even if the transmission was replaced 6 months ago, it could well be going bad again.
- Jack
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2014 F150 Platinum SCrew 3.5L EcoBoost 4x4 with SCT programmer
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