The solution to your specific issue should be addressed by someone that knows what they're doing.
If you were my customer, I would go about that by returning the truck to stock, then update the computer programs in the truck with the latest Ford flash programming, then reinstall the tuner. That said, I'm not a fan of H&S. I've seen them break too much stuff. I'm and SCT Dealer and have been since 2002.
What did the guys that you bought the tuner from say?