First question, do you still have the auto-petcock or did you or a PO remove it?
The below is based on your description, pics would help a lot. Heck, by "smaller tubes" you could just be referring to the tubes that connect to the bottoms of the bowls that just guide fuel when the bowls overflow. If that is the case, then everything I'm saying below is wrong.
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1. Incorrect. The nipple on the top in between the #1 & #2 carbs is where your your fuel gets into the carbs. This is either a direct fuel line from the tank if you don't have an auto-petcock, or where the fuel line from the auto-petcock hooks up to the carbs if you do.
2. Can you get a pic? I think that you're referring to the vacuum sensor for the auto-petcock that can be capped if you don't have an auto-petcock or hooked up to the auto-petcock if you do have one.
3. The T between carbs 2 & 3 should be hooked up to a hose that runs under the air box. It just needs to vent to atmosphere. You could probably leave it with nothing on it, but I wouldn't want anything falling into it. Don't run the cable into the airbox. Yes this is pretty much a breather.
1981 CB750K with 900 cams
90K KM's, rebuilt head, rebuilt carbs, upgraded valve stem seals
My wife's recipe website that I'm trying to help promote:
Strawberries for supper. Yes, I am a lucky man.