Answers
1/ this goes to a spigot on the air box. I would blank off the air box spigot and put a fuel filter onto the end of the hanging hose once I have made sure the hose is clean.
2/ this is an atmospheric pressure inlet, I would put a short hose on this with some sort of filter on it. Maybe some neatly fitted air filter foam stuffed into the hose.
3/ since you are already working on the bike, I would take the crankcase breather out of the airbox and route the hose up high and put a filter on it. Make sure to blank off the spigot on the airbox where the crankcase breather used to go.