I fill the sides with rtv, then I shove a piece of precut 3/32 or 1/8 welding rod in there and it forces the rtv out slightly. I like seeing the expanded bead on retainer from top to bottom of the edge gap. Just my twist on this personal subject. I also put the seal in 12/6. And I wouldn't drill the holes seems that could add to the alignment issue. I have reduced the height slightly by flat sanding/milling approximately .010 off for a little extra crush. Most of the time its just the black rubber seal.