If your keyboard is a bit too tall to fit on the tray at the normal setting (4.25"), you can lower it in order to have a 5.375" vertical clearance.
Looking at the tray wings you'll see 2 silver L-shaped brackets that attach them to the bottom of the desktop. On the wing side there are 4 screws attached. To lower the keyboard tray, remove all of the screws and attach the bottom two screw holes of the silver bracket to the top 2 holes on the wooden tray wings (which will leave two holes exposed and unscrewed).
Please see the image below. You will simply shift the L bracket in the direction of the arrows so that the green dots are where the yellow stars are. Hope that clarifies things!