TeamTEOR, the distance from joystick to buttons is, as usual here, personal preference. I would look at a cab you feel confortable with and measure or create a mockup of your own design; there is no exact number to be placed here. Also, some like to angle there buttons; I personally dont, so a lot of personal preference. Just remember this is your cab, you will be playing it, so do what you like not nessecarily what everyone else has done or is doing, that is the GREAT thing about building it yourself...
As for you joystick recess, I used 3/4 MDF and I don't know the exact depth I recessed but it was the depth of the joystick rim. Came out great no complaints or issues. For the buttons, I bought them from HAPP and I don't know the PN but again 3/4 MDF no recess for the button and it's fine.
Something you may come to if you are going to use a lexan/plexi overlay. I didn't attach my lexan to the CP with anything, no screw or tape, nothing. Once the pushbuttons were installed they hold it on place perfect and no movement what so ever AND not bulky screwes or bolts sticking through my CP. I did you a rounded router bit to round the edge of the lexan so it looked nice and smooth; loved it ever better once I saw it completed.