Reading the plans about the gunwales, if I am going with both inwalland outwall are they 1/2" thick each for 1"total or 1" thick each? Where the gunwales go I understand not to put glass cloth in this area but do I need to protect it from epoxy as well to get bare wood to glue to? Thanks
1/2" in and out should be plenty. 3/8" on both with a stout thwart will do fine as well.
You can install the gunwales over the glass. Not doing so and gluing directly to the wood is just an additional quality step. Like tie your shoes... do you want to double or triple knot?
When you glue the gunwales to the bare wood, the epoxy that is in the glue will seal the wood nicely. Just be sure to coat any bare wood surfaces that are exposed.