The fuel lines, they go to the 2 "T"s that you replaced between 1&2, and 3&4, That is 7mm fuel line, hard to find around here in rubber so I use clear /tinted 7mm fuel line that would normally be found at snowmobile shops.
The other 2 openings that you had in the pic between 2&3 as far as I know takes 2 8inch tubes and hangs out around the aircleaner box not connected to anything else, does not return fuel up to the tank, just hangs out in space just below the carb bowls.
All the bikes I ever had came that way and were rebuilt that way I never questioned why, just did it, maybe someone here can explain their reason for being , I can't say that I've ever thought about them before.