14 Foot Flat Jon Mod

[Shotcaller]

Hey guys. My first time doing a mod. I've read so many threads no this site that my eyes are crossing. I think all of this research has answered my questions. I do want some advice and reassurance. The boat I bought had a deck on it but was way to unstable to me. The boat is 42" across the top at the front, but only 36" wide at the bottom. I understand that with a boat this narrow that I need to keep the center of gravity pretty low. So I tore out that deck and plan on doing a build that I've seen a couple guys do. Gonna have a small deck on the front for trolling motor and depth finder. Also use the underneath for battery and life jacket storage. Not to stand on. I already cut out the front bench and plan on putting down a plywood floor. Seat at front on floor and another seat on bench at back. Rod holders on carpeted plywood on the sides. Also I plan on cutting some lids for the rear bench for tackle storage. Here are my questions.
1. Jb weld any leaks and then bedliner in floor? Will this be good enough? No major leaks right now.
2. Is Spar Urathane the best wood treatment? Can it contact the aluminum or will it ruin it like Thompsons water sealer?
3. If I paint the entire boat do I need to prime it in an "etching" primer?
Thanks for replies!

 

[Shotcaller]

The next pic is after deck removal. After that is after bench removal. Finally the last pic is how I plan on setting it up. The 2x4 up front is the front raised deck. The tackle is sitting where I will cut out top of bench for tackle storage. All advice and comments are welcome.

 

[Shotcaller]

Second pic. I don't know why they are posting sideways!

 

[Shotcaller]

Final pic. The setup.