You would go to a big throttle body if you were running a blower with a lot of boost. Otherwise they just cause tuning and drivability issues, they take some serious time and knowledge to get working properly. Most of the aftermarket TB are also not made to the tolerance the stock ones are so they inherently don't work as well. On a stock bottom end combo I wouldn't bother.
A tune can net power if you are increasing octane, by increasing the aggressiveness of the timing tables. They don't magically increase air delivery to the engine. That is purely a function of engine efficiency (mechanical). The gains from tunes usually come from changes in the pedal sensitivity, changes in shift points and transmission logic, and power enrichment. A tune will net power under the curve, but not too much peak if you keep the same octane. These trucks already pull timing pretty much all the time on low grade gas, so they are optimized there. Throttle angle is at 81° max from the factory, optimum is 82° so there isn't much there either. Ford did a good job on the tune in these trucks. There isn't a lot of meat on the bone, but you can certainly make what is there a little more aggressive/responsive.
You can net some power out of a CAI, but it isn't much, and it isn't worth while, the stock panel filter is the way to rock it off road. They pull good cool, clean air and there is enough filter area to fill the engines need.
Long tubes help, especially on the low end. Peak gain isn't huge but area under the curve is, which matters with these trucks, especially in third gear on the dirt.
You can gain some power on e85 as well, just have to find someone to tune for it and a source for the fuel.