The three tubes you can leave uncapped w/o a problem tho I recommend capping off the ribbed one closest to your air filter to help prevent water/dirt frm entering. The other two are simply vents. There's a fourth under the carb on the bowl itself which is just an overflow drain.
The shifter lever is used for the enrichment circuit (same effect as a choke, but allows more fuel instead of cutting off air) - when ya pull on the cable it opens a port for more fuel to enter the carb
Here's summore info