I know the dirt is coming up from the road and in from the rear inner fender area. How can I stop this? When I open my gas door I always have sand/dirt sitting on the ledge. Sometimes a little but mostly alot when it rains or in winter.

Should I seal it up from the inner rear quarter panel? How do I remove hose/gas cap square part. Should I use Silicone? Anyone have any advise?

you could silicone from inside and outside, then maybe a lyer or rubberized undercoating in the QP well