Automotive Rust Repair...What You Need To Know! 

Treat the insides with surface shield and finish it like oem

Certainly not a bad idea! there are definitely areas we can improve what the factory has done to prevent future damages. However, in your case you'll have to ensure that you are not creating an area that will allow more debris in. There are one way valves and removable plugs that can be used to help drain and prevent further problems. . . our suggestion is that you design your modification around something of that nature.

@@trendlessdesigns And that's a great point. A gromet or plug of some sort could be fashioned and used as a drain/inspection hole on one end of each inside panel of the rockers (park on a slight hill to drain). Thanks.