those hoses are forthe ventialtion of your gas tank and the over spill for it. they plug into the bottom of the tank. as far as the clutch goes, did you take the crank casr covers off to get them painted? the clutch is the othr side of the bike btw, that side is the charging unit for your battery. if you took the clutch cover off, when you put it back on you have to turn it so it catches with the clutch cable. show me a pic of the other side.
oh thats the shift linkage. try tightening the top and bottom bolt. might want to use lock tight. but you will have to adjust the linkage a bit to get it to shift and feel right. i had this same problem when i was going our for a ride and the bolt rattled loose. i fixed it on the side of the freeway.it was riding fine the other day. today it went blahh on me. that green metal bar moves freely and i can pull it slightly in and out of place. i wont be able to post another pic untill tomorrow since i left it at my friends house.