Ya those weathertech flaps have very little when clearance even considering everything else is stock. Who do your powder coating? Called a couple of places downtown the other day and nobody answered the phone. Another one of my buddies said there's a place down in Spring Hill that does a good job.
My buddy took mine in with some other projects we are working on for my truck...to be announced soon. They did a great job, here is their link.
Liquid & Powdercoat Finishes
Red Hot Trail Boss