Here the central bolt standoffs get the same treatment as the outer screen. Just grind off the top end of the standoffs until the height is again about 1/32" less than the thickness of the filter element. Do try to keep the end of the standoff flat and perpendicular to the shank so the cover will lay flat when installed. And when your finished here you should run a 5/16-24 tap into the part to cut the threads a couple of turns deeper to allow installation of the cover bolts without bottoming out on the threads.