The line that pulls vacuume will still be a vacuum leak if you put it into your new intake. It iddn't go into the intake tract on your sock setup. It went to a bimetal valve that would open when cold that would then pull a butterly open to let the heat from the heat riser into the intake. It was not a vacuum leak, which it would be if you put it into your new intake.
As for how you plug it, I dont' use screws, I use golf t's but yes you can plug the line, it doesn't matter.. Heck you could plug both lines right at your intake and it would be find.. I was just trying to say you don't need the lines, one you can remove, the other you just need to make sure doesn't become a vacuum leak.
~Mark