My RT1 carb intake has 3 ports on the bottom of the intake side. The one on the left has a brass plug, the one in the middle is open and clear, but  the one on the right may be blocked I think. I'm don't have a clue to what the purpose of this port is or even if it is supposed to be open to something. If I spray carb cleaner in it seems like it is not going through to anywhere. Is it supposed to be open? What is the function of that port?

Each of those ports is under vacuum air when slide is down. When engine is running, engine side has some degree of vacuum and a venturi affect created by small space of air flow under slide (cutaway) which causes a misting and vacuum on air screw and idle jets. As slide/needle progresses open, the big hole in the middle progressively pulls fuel from needle jet via main jet. As slide goes WOT, airflow passes across needle jet, pulling fuel from main jet.

In any case, I think the hole in middle might be the idle circuit, ie airflow goes in to bowl (which now has vacuum and atmospheric pressure near exit) and only has one way out, through the idle or slow jet. The air screw progressively adds/subtracts airflow from same area idle jet provides fuel in chamber. I believe the air screw is the far left. choke circuit probably right.  It will be obvious when you look at it. Open the choke or air may not flow.  I call it a choke.  Its really enrichment.

Note, you may not be able to blow through the air screw if the air screw is dialed in tight. I would take it out to clean it.

If I have not explained this correctly, someone please edit. Its late.

Rachter, you're fine.

The Mikuni carb has variations.  Some have the idle air screw and passage on the left and some have it on the right.  They only drill the side with the air screw.  (You'd be in trouble if the hole on right side went anywhere, it's supposed to be blanked)

Sometimes they block the actual idle air passage in the bell (in your case on the left) with a brass ball and the idle air passage gets its air from somewhere else...  often the idle air passage is simply connected to the center air passage with a short connecting hole very near the end of the bell.

The center air passage goes to the needle jet.  On your RT1, Yamaha used a "primary" type needle jet (sometimes called a "two stroke" type even though that's not universally true).   As RPM increases and throttle is over 3/4 open the center passage actually richens the mixture slightly.  Seems counterintuitive, but that's how it works.  Air flow through that center passage literally pulls more fuel from the float bowl.   

Thanks Guys. Mark I have looked for an explanation for what those ports do for a while now online, with no luck. Thanks for a clearing that up.
Dick