The line that goes to the intake runner, just cap it off at the runner?
Yup.
If you use a vacuum cap no sealer should be necessary. If you stick a screw in a piece of hose you might want to seal the threads.
ok. Same size screw as the other side? (I did the emissions removal)
I think so.
Is the hose the same size?
You can get a nifty little rubber cap that looks much cleaner.
I'll look into that