See my responses below in blue, note that I didn't address the questions about flooring that I don't have experience with:
I plan to use 5/8" Marine Plywood and treat the perimeter with epoxy / waterproofing to better protect it.
If I fix the leak I just think the Coosa Composite at $215 a sheet not including delivery is a bit of over kill.
I used marine plywood on my floor repair as well, but in retrospect, I figure plain old construction grade plywood from the big box store would have been just fine. It seems that it is more important to seal it than what grade the wood is. Are you replacing your entire subfloor, or just the back sheet?
I think I will need to remove my belly pan to gain access to the chassis so I can install the elevator bolts.
Is this correct? Yes
On the plywood repair the 5/8" material is needed to fit inside the C-Chanel?
I don't know about your specific year, but measure what you have, and match it.
Will I need to remove the inner skin at all? You will need to remove the lower sections of inner skin so that you have access to the bolts and screws that hold the C-channel down.
If I do I have the fuzzy carpet type of material on the inside of the walls will this re-glue down? Yes
Most importantly how do I fix the leak? Do I need to remove the beltline and or bumper to correctly seal this joint?
There is a well documented fix for this issue. Do a search for "rear end separation," and you should find several threads. To sum it up, you will create an "L" shaped piece of aluminum flashing that goes up into the skin, and the lower part of the "L" extends out toward the bumper trunk. This will direct the water away from the joint at the rear of the trailer. You will need to disassemble the bumper trunk and beltline to do this right.
Do I seal it it from inside the trailer after the demo is completed? Seal from the inside and the outside.