Honestly, I would not go with your stated plan, unless you plan on trading/selling the truck immediately afterward.
The longest lasting repair involves cutting out and replacing the affected panels, either whole with OEM parts, or with aftermarket "patch panels" that would span the area known to rust (cut out the area above the wheelwell and weld in the replacement partial panel). Just treating the outside surface of the affected panel is a waste of time, as by the time you see the bubbles outside, the inside is already gone, the problem starts inside and will quickly visibly return unless the whole affected area is replaced.
Wheel flares actually exacerbate the problem because they hold moisture. The panel needs to "breathe" so moisture dries inside the panel. Wheel flares prevent air circulation. Here in PA, I cannot tell you how many times we've gotten a pickup truck (mostly Dodges with factory flares, but also GM '07-'13 with aftermarket flares) in the shop with bedside damage, a wheel flare takes a chunk of rusty bedside panel with it when it is removed, totally complicating a collision repair. The rocker panels and cab corners rust out on Fords of the same era.
The '07-'13 GM trucks were engineered during lean times at the corporation. I am not sure if it was a metal quality problem, or a lack of designed-in drainage function to prevent the build-up of dirt/moisture inside the bed panels, but the problem is way too common (with or without aftermarket wheel flares) at least here in my area of the country.
That is a beautiful truck, sorry you have to deal with this. It's too soon, imo!