I would not use silicon except a small dab on the corners for the timing cover to block and rear main seal housing to block. Install dry or better yet a thin film of oil on the raised seal. Those that use Hylomar have it figured out. I would not drill any additional holes. Avoid silicon, or anything that cures rigid. You'll regret the choice to use silicon, especially Right Stuff, on the day you need to remove the windage tray. It'll require dynomite to remove.