Bigger flares as mentioned may help, but that's generally the price you pay for larger tires and a wider offset. You get more stuff blown up by the tires and compounded by having to remove your flaps.
You have at least stationary running boards which will prevent most of the potential damage to your rear rocker panels/bed sides from rocks being thrown up by the front tires.
I think your best bet for an effective yet attractive solution is PPF on your lower door panels to prevent rock chips, however there isn't much to prevent mud/dirt being thrown up there.
By the way, your truck looks great!