What are all these holes for?

I figured I would just plug up the ones I was not using I just wanted to make sure I was not missing something. Yea I dont plan on using the cork gaskets for the front and rear seals. They were on when I took the old Torker off and were all dry and cracked. So I just pull the pens and put down the RTV and let it set for a while then put the intake on and bolt it down or should i put it on and bolt it down right after I lay the bead of RTV. I don't plan on driving it for a couple days after I put the intake on btw. Although I do need to change the Tie rods and ball joints on my truck in a few days so the dart will be on daily drive duty next week.