Your post was kind of convoluted but basically if you top you have to make a hole through the top panel that is are enough to fit the base of the joystick. In addition to that you must make a recess around that hole so that the mounting plate will sit inside of it. When you’re done with the top panel it should look something like this:
When you put the JLF in that area, the mounting plate and joystick will fit in that area and the mounting plate will be BELOW the top panel. NOT sitting on top. It should not even be flush with the top panel otherwise it will be sitting a little too high.
Hope that is helpful. If you want, you can read my other thread and find out more, but I do not suggest you follow it since it’s a more advanced method of building sticks that only TheRealNeoGeo (you could call him my mentor, heh heh) and myself use, but there might be some other helpful information for you.