On our JKU I had the local wrap shop apply a layer of PPF 1/3" high along the entire sides of the truck in addition to the entire exterior hoop of the flairs. They cut by hand (basic shapes) and had it done (and flawless) in 2 hours. Cost me $300 and was worth every penny, then some.
Flairs will help but there is no coming back from DIY touch-up on what appears to be an otherwise new truck. Might be worth taking it to a body shop, most now cover PPF as well and may be able to add it in at a discounted price.