I would start by verifying that you have a full transmission. My truck came from the dealer a quart shy and this could have an effect. Tow Haul will primarily affect the torque converter and how it locks up and how and when it releases. This is designed not for smoother shifting but to keep the transmission operating cooler as more slipping adds more heat.
Check with Ford to be sure that there are no service bulletins for either the 2012 or the 2011 trucks with this transmission. You should be able to check online.