Rust under bed rail caps

The previous owner of my truck had a Leer cap on the back for the last 7 years that he owned it. From the weight, rubbing and snug fit of the Leer, it seems that moisture built up under the bed rail caps and eventually started to rust. The weatherstripping on the hatch also seemed to have rubbed and created moisture causing a rust line on the tailgate.

Now that I have taken off the Leer and moved to a tonneau cover, I really want to get the rust looked at and hopefully repaired before it gets worse, since its now a lot more visible.

My questions are:

1. Has anyone on here ever had rust build up on under the bed rail caps? If so, was it a costly repair?
   
   
   
   
   
   
   
2. Does anyone know of extended bed rail caps available for the 2nd gen similar to these below on a 1st gen? I have seen many available for other generations, as well as other truck brands. (Photo credit: Kohan21n)
   
   
   
   
3. Does anyone know of extended tailgate caps available for the 2nd gen similar to these below on a 1st gen? I have looked into the KB VOODOO, but I don't think it hangs low enough to cover the rust on my tailgate.
   
   
   
   
   Your input is greatly appreciated!

 

i have a cap on mine and noticed it was rubbing the paint this year. but it's winter out so not much i can do now. When spring comes cap will be coming off along with the bed rail caps and i will be taping off a line and sanding/priming/and painting with bed liner to keep it from happening. I know there's a thread somewhere about it all but some guys put silicone under the bedrail caps.

 

I had actually seen another member on here that had bedliner under his caps and it looks perfect plus provides more protection.

I was wanting to do this myself as well but one side has too much bubbling and hangs down too low to just sand and spray.

Picture of the member on here for reference

 

Any more info about the thread mentioned? I couldn't find it through a few searches. Mostly just looking for info about how to remove the caps on the sides of the bed. I pulled all the bolts that hold the rails in and popped the two button clips off but still couldn't get the cap to budge hardly at all. Decided to put it back together for now and find out how they are attached before I damage something. I will probably do the bedliner under the caps or fab some steel and make the tops of the bed sides more traditional without the caps if it's feasible.

 

Mine is a second gen and other then a couple of side clips the rest snaps into the top of the bedsides broke a couple of them but I have a camper shell that sits on top so I wasn't worried about them coming off

 

Snaps in from above? Is there a way to release the snaps other than just pulling up on the cover until they release or fail. Mine is a 2nd Gen, too. I just havn't updated my info. Only had it 24 hours or so and didn't even think about my profile! oops. :derp:

 

I've been planning the same for years.... Still haven't done it

 

Just to play devil's advocate, is it worth doing anything about it? It is a 13-14 year old truck. That is beater territory for most vehicles. I'd let it ride, it'll never cause you any problems outside the cosmetic for the life left in the vehicle.

 

If there's a way to release it no idea. I just pulled up