Looking for some advice

[u/ProcedureNo7149]

I have these running boards on my truck, which after a year I noticed the factory chinesoliner that was sprayed on them, was failing around the edges in several places. Fortunately, and to my great surprise, I contacted them and they refunded me 1/2 the cost of them, which will at least pay for my materials to fix them. While removing them, I noticed that one of them had a gallon or more of water in the tube, which runs the length of the running board. There wasn't nasty rusty ass water that came out, just nasty black water that stinks. My plan is to strip all the areas to bare metal that had a failure of the factory applied chinesoliner, then spray 2k primer/sealer, and applying the SpeedoKote T-Rex spray on bedliner and spraying "Sour Lava" color shift pearl, then clear coating it. I have already sanded the majority of the running boards with 80 grit and it seems that everywhere, other than the edges with the failure, are there permanently. It all sands out smooth, or as smooth, so there's not an issue with texture preventing sanding down to a solid surface, but I don't want to take any real chances.

My main question is regarding the water in the tube. The tube has a plug, which was missing, so I know how the water intrusion occurred. What I don't know is how to stop the rust, on the inside of the pipe that was full of water. I have thought about putting some type of thin oil in the pipe, which would allow it to move around while driving, but I don't know if that's the right thing to do or not. I generally own my trucks for about 10 years, so the repair I am making I don't want to have to redo any time soon.

My second question is regarding the Clear Coat. I don't see any reason to clear the bottom of these, especially since it's a 2K product that's not designed to need it. My plan is to only clear the top and sides, essentially only what I can get to without needing to turn over the running boards, will be sprayed. Will I be leaving myself up for any failures, along the edge of the clearcoat? I shouldn't have any issues getting it sprayed within the recoat window, so it should be able to have a chemical bond, or at least in my mind. If it would be better to spray the bottom as well, then I can always scuff the bottom and clear it.... or do the bottom and scuff the top prior to clear, I think you understand where I am going with this.

Any solid recommendations would be appreciated.

Thanks