Thanks to all the for all of the advice. A couple of notes and comments:
The reason I was considering using Gorilla Glue was so that there would not be any tapering or countersinking bolt holes. Additionally, the chances of my CPO not sticking due Yes, I do realize that to some it is not that big of a deal. I, however, am brand new at the woodworking thing so anything that prevents me from screwing up the better.

I, as a novice at this, was just looking for other options. This board has so many experts that have been doing this for years that I really do value everyone's opinion.
The other comment I find kind of ironic is that many people have said that the "professionals" would never permanently mount a joystick. What I find ironic about that is that those same people have no problem with countersinking bolt holes and putting a CPO and plexi over them. Some have even used wood filler over the joys to ensure they are flush. I will give you that it is not absolutely mounted forever in that case, but I would argue that it is probably as much effort to scribe out the sides of the joy that are glued in to loosen and get it out in what I was suggesting, than it would be to remove the buttons so you could remove the lexan so that you could remove/ruin the CPO, so you could remove the carriage bolts, so you could replace the joy in the other widely acceptable method. Seems pretty darned "permanent" to me in either case - glued or bolted flush.
I am really now leaning towards Dowdy and leaving my bolt holes exposed - for a variety of reasons:
1. Almost every arcade I have ever visited has bolt heads showing.
2. I have a 7 year old who has friends that will be playing this cab and the need to replace joys will likely arise.
3. It simplifies a number of things for installation including the fact that it would take care of the Lexan staying down issue.
I wanted to say thanks again for all of the thoughts and advice. It really is invaluable information. Cheers
