There is a required driving period after a truck has been reflashed. This allows the PCM to set the parameters for your driving and local area. There is a new FICM reflash that helps prevent FICM issues, by your post seems like they did that as well.
Drive it like you normally would over the next few days or week. Hopefully there won't be any additional issues with the way it feels.
It's an adaptive memory.
Drive it like you stole it.