Never tried this, but I think it would work... Mix up some thickened resin to the consistency of like ketchup so it will stick on a vertical surface but not so thick you cant easily work it around (only cabosil is needed, no need to add chopped fibers but it wouldn't hurt). Roll or brush this onto the wood and surrounding glass on the cap in the area you will apply the glass. Then, I would lay out a table as stated and wet out the glass on that surface (using regular resin, not thickened), let it sit and work it with a roller until its fully saturated and any binders are dissolved out, then work it with a squeegee to get out all the excess resin. Then transfer that over to the cap, shouldn't be any excess to drip in your eye and ruin your Guns'n'Roses T-shirt. Use your hands/roller/chip brush, to bed the glass into the thickened resin on the cap and your done.
On the topic of reinforcement for the tower... go big... I wouldn't hesistate to add 3 layers of 1708 over the wood overlapping each layer by 2" on each side. A wake tower pulling a 200lb guy on a tube is A LOT! of torque/force on those mounts. Say the tow point is 4' above the attachment points, it wouldn't suprise me if thats putting a few thousand ft-lbs of torque on the tower assembly mounts. I've seen a lot of pictures this summer of guys ripping tow points out of their swim decks from towing a tube.