To get anything to stick to the glass you need to sand it to get the waxy surface off of it. Coarse discs don't clog so bad. Give the wood a scratch up too, while your'e at it.
I have always used Epoxy resin to do this, marine shops will also sell you the glue powder to mix in the resin to thicken her up. You can also buy a micro balloon powder to make a filler with the resin for when your'e finishing off.
Recently I have been using builders glue, which is a single pack and comes in a gun cartridge, to glue wood onto the glass. Works like hot damn, you still need to sand the surface and of course the fit up needs to be good, the builders glue won't gap fill. Sticks fine, but.
If you have gaps use epoxy thickened up with glue powder, you can stop it running out as it sets (it goes runny as it sets) with race tape "dams"
Use exterior glued ply for the floor, doesn't have to be treated since you will ultimately glass or resin coat the whole thing to waterproof.
Chop Strand Mat is the stuff to use to reinforce, say 4oz. Epoxy doesn't "wet out" the glass very readily so while you are at the marine shop get a lay up roller, which looks like a stack of 1" washers. Rolling the wet glass really helps the wetting - if its not wet properly strength goes away. Get a couple of gallons of Acetone as well, its a solvent you'll need to clean up your brushes and rollers.