Sorry I vanished in the middle of the saga, life happened, this project went on hiatus several times, but I just finished it.
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The 200lb lift struts I originally used proved insufficient once the aluminum was installed and I had to modify the strut geometry and upgrade to 300lb lift struts. That got it working exactly how I wanted.
I went with the suggestion to spray the aluminum with bed liner. I used the Raptor tintable bed liner kit off Amazon. I did not realize, this stuff is marketed toward the "I want to spray my entire jeep in bed liner" crowd and it's probably great for that purpose, but if you're expecting a 1/8 thick coating like a BED LINER is supposed to be, you'll be disappointed with this product as basically a rugged paint, and sprays about as thick as a two-part epoxy paint would. I bought the 1 gal kit sold as a solution for lining a typical bed and used the whole thing just on this sheet of aluminum and it's about 0.05" thick. I inquired with raptor about spraying another 2 whole kits on top it and they said not to, or it would Crack. Also be advised this stuff will NOT hide seams or dents.
I got the color-code-matched paint tint from a local automotive paint shop and I mixed it too rich so the bad liner is a little too dark, but close enough for me not lay awake at night thinking about it. The metallic flake in the tint does not show in the bed liner, but I think it might help in reflecting sunlight as the inside of the bed stays cooler than inside the cab when parked in direct sunlight, which I did not expect. I thought it would be sweltering in there.
Here are some pics of the final product:
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