i put the 4 way stick up high on my first 2player panel, and it was uncomfortable to use. i then removed the trackball and spinner and put the 4way stick in the center where the trackball was, it was much better that way. my friend just built a giant 4 player panel and the 4way stick is pretty high again, above player 1's buttons, however due to the added depth of the panel, it feels pretty good like that. the biggest problem with mine was that there wasn't enough space between the top of the player 1 buttons, and the 4way, so you had no where to rest your hand. i just convinced my wife that i need another cabinet, so i am going to make one with two 8way sticks, and the other cabinet will have a 4way, spinner and trackball...that way none of the panels are overly crowded and you should be able to use all of the controls really well.
i think that in your case, as long as the panel is deep enough, you shouln't have a problem. just for reference, my friends panel is 18"x48"