Most of these can be found through the Search, but I'll try to help.
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1. How would i get the top to fit against the seat when it is locked down ?
Use MDF for the top part of the box. Just measure out the size.
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2. I put masking take then tin foil on my floor and make a mold of resin and mat ? and by doing so do i just put pieces of mat down and cover them in the resin ?
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Tape down the tin foil to the floor, cut some mat/cloth and lay it down, then apply the resin. Some say to apply the resin then lay down the fiberglass, but that can be messy. Do 2-3 layers of fiberglass then let it dry. It should be sturdy enough after the 3rd layer to pull out of the truck. Once out, apply more layers (in 2-3 layer increments) until it has almost zero flex.
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3. Should i make a structure out of MDF for a box ? like a face piece and run strips of MDF or dowels down both sides and the top to have something to stretch the fabric over ?
Not 100% sure the question, but I did the bottom of my box with fiberglass since there were a lot of curves, then I did the sides and top out of MDF. No fabric, no dowels, just some fiberglass, MDF and a few late nights.
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4. What is the best fabric to stretch ? i saw someone mentioned a bed sheet ?
Fleece is the top choice, other fabrics, such as an old tshirt, works as well. It all depends on how big of a structure you are making and/or how cheap you are.
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5. How much stuff will i need to make a box to fit 2 12'' CompVr's?
No clue, check their website for the recommended volume then figure out how much of your box will be fiberglass.
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6. What release agent would be good so i can get the bottom mold off the floor to finish it outside the truck ?
Tinfoil will allow you to pull the mold right up and out, once out just peel what you can of it away. As I said before, 2-3 layers *should* be enough strength for you to be able to remove it form the truck. If it is huge, it might take more.