1) No. The 2 plastic nipples are the sub-air filter ports that have to be connected to the squared filter box to allow the vacuum pistons of the carbs to operate correctly. You do still have the sub-air filter box, correct?1) is it okay to leave these just open or do I plug it with something?
2) Not really sure what to do I appreciate any and all help, thanks!
3) there’s still the one hose that connects to that yellow reservoir thing that’s part of the air cleaner systen, but if I were to connect that one then the other side of the carb would be left still open
3) In your last pic, the hose in your left hand should not be attached to the 'yellow reservoir thing' (the yellow reservoir thing is for crankcase vapors), it should be attached to the sub-air filter box.
In your last pic, it shows a vacuum operated air valve that is present on California bikes (that's it between the yellow thing and the green wire/hose. With what you are trying to accomplish (with velocity stacks) the easiest thing to do would be to eliminate all of the emission control system components on the bike first and work from there.
There is no need to eliminate the sub-air filter from the carbs. They need it to function properly.
As a fail-safe, you always have the option to cover the plastic vent nipples with lawn mower green foam air filter material held in place with zip-ties.