I was putting in new spark plugs today and noticed these two ports open.

should they be plugged or plugged into something?

It's a 98 RR 4.0 SE

Here's a pic of both.

I did have the air bags removed and springs installed last year by the dealer.

 

the first and fourth pics are your cruise control vac servo....cap off the tee fitting for now.

the second & third pic is a vac hose that should go from the plenum fitting in the pics to a fitting on the passenger side valve cover....if you cant get a hose soon, you could cap off the fitting on the plenum for now....other wise you will have a vac leak.
It's probably wise at this point to look EVERYTHING over and start making a list