A mockup made from cardboard and dowels goes a looooooong way on control placement and layout.
I have my joysticks mounted beneath the panel. I routed out the MDF of the CP to allow a good fit for the joysticks. Then I bored a hole for the stick to go through. In my case I have Ikari Warrior style rotary 8-way sticks and I wasn't able to take the top off the stick. So the hole size in the CP had to be large enough to pass the stick top through. I think it was a 1" diameter hole.
I used countersunk machine screws to mount the sticks with nuts underneath. The artwork covers the screws and the clear acrylic sheet went over the artwork. The buttons on top of the acrylic are the only thing that hold it in place.
Restrictor plates are nice, but I don't have them. I'm in the process of adding a super cheap (i.e. I took it out of a broken kids toy) dedicated 4-way to the upper deck of my CP. Probably less of an option for a cocktail style cab.
As for clearance to the glass....again, a mockup is an invaluable tool there.