Chris,

That's the aux air regulator. When the water is cold, it routes some air into the intake manifold, bypassing the throttle -- that's D-jet's "fast idle" function. When the water warms, it closes (or should close).

Leave it right where it is -- no harm.

Don't use RTV on the freeze plugs covering the injector holes. Just put the into the holes dry, but clean the holes really well first. When you flatten them, the sharp edges of the plugs cut a tiny bit into the edges of the holes and that seals things up fine. RTV would actually be in the way of this, and it's corrosive in the long run.