There are all sorts problems that you will encounter on a project like that if you do not physically mold your part from the truck it’s self. I strongly advise against any attempt to use wood, foam, or any forming system that can change shape due to temperature or humidity. I have a method that I use to make exact duplicate parts that might help you get a perfect mold of your bed rails. After you have that you can shape the top side (the part you see) any way you want and it will be a perfect fit to your truck.
You will need several products that you do not likely have.
Polyease www.tapplastics
Vette Panel Adhesive/Filler www.evercoat.com
Vinyl-ester resin www.tapplastics.com
Double sided foam tape
Small spiral roller www.tapplastics.com
And some products that you probably already have.
Polyester resin
1.5 oz. fiberglass matt
Small brushes
Masking tape
The process goes like this. I make a fiberglass mould by glassing rite over the part I want to duplicate. Forming a negative. Then I peal that off and lay glass inside that negative forming an exact duplicate of the original.
For your part all you need is that negative and then you can build on top of that.
In my example I needed to replicate the chrome rail that runs along the top of a 57 Chevy door panel. After I had my replica I was free to modify its shape with out damaging the very valuable original part.
Step one
Here is the original part. Notice that I have used double sided tape to outline where the mold edges are. This helps me demold my part as well as give me a visual line to grind to after I demould my part.
Step two
Spray the part down with polyease (release agent)
Next I mix the Vette filler with standard polyester resin. 4 parts filler one part resin and mix in only cream hardener no liquid MEKP. And brush on the mix.
Step three
Using Vinyl-ester resin apply 2-3 layers of fiberglass matt. No sanding required. Use a small roller to thoroughly saturate the matt. While still wet I suggest that you lay down some angle iron and let it bond. This will keep your negative from warping. With a long piece simple gravity will warp your part once off of the truck if its not reinforced. Angle iron is cheap and readily available.
Step four
Pull your negative from the positive (your truck). Use compressed air for this. If you get just a little air between your parts they pop rite apart. As you see in the pic I now have a perfect negative. No warping, no cracking, no pin holes, no sanding required. Denatured alcohol works well do degrease all parts. At this point If I were you I would shape the top surface of your new panel using the vette filler as your bondo. Prime, and paint.
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The remaining steps on my project
Now that I have this flawless negative I respray with polyease and paint more vette filler/resin mix into the inside. Then fiberglass matt. When I pull my part all I have to do is degrease, prime and paint. No body work!
This is the black part at the top of this door panel.
Warning
Standard body fillers and polyester resins will not work in lieu of the products that I have suggested here. They are unstable when exposed to heat, moister, and display to high of a shrink rate for this type of project.