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Just paid off my truck ('99 250) and got "permission" to start fixing it up! I'm currently researching paint, but a bed liner is next on the list. I currently have a plastic drop-in but want to move to a spray-in. I'm between Line-X and Rhino and wanted to see what others have experienced with either of them. I don't want to DIY it because I'm also going to have it run along the base of the body and the bumpers as well.
You'll like this option. I can't say as to what to go with as I bought my box and it was already lined. After I sanded it down and had it primed though, I got it painted, and did as you described and had my rocker panels and lower box sides painted with liner.
The only thing I can say is find a reputable body guy by you and have him do it. The guy I had do mine did a special coat on the panels that was thinner and smoother than usual, but still holds up really good.
I highly recommend Line-X. I routinely haul full 55 gallon drums in the bed, and they get rolled and dragged on it all the time. I'm really surprised it's not more beat up than it is, but it holds up really well. There are a couple tears where some drums were tilted and dragged, but that's to be expected. I doubt there's anything that could hold up to that type of abuse other than a plastic slide in bedliner. It was in the truck when I purchased it used, so it's at least 8-9 years old. Great traction when it's wet. Based on what I've seen on a friends truck with the Rhino lining, his seems a lot softer and doesn't take abuse nearly as well as mine.