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Did you do the install of the Whipple yourself?
My guy definitely agreed the new gen Ford ECU's are hell. Lots of people had issues with the new 5.0 Mustangs too, and ruined enough engines that Ford issued a TSB to dealers to deny engine warranties on tuned cars.
My tuner's base file tune he gave me just to "get it running and drive up here for the tuning" handled the throttle body swap just fine, before they ever really touched the tuning.
Loaded up the base file with the standard SCT flash tuner, so I assume they are using SCT software.
You may have your local guy call Fastlane and they may sell him a tune that he can tweak. Dont know, but worth a call. They had just finished another in house install of Whipple Raptor that same week.