Whatever it is, it's obvious that it's a lean issue - what's surprising is it doesn't need the choke until AFTER it warms up - somewhat opposite of normal.
That tee is just a vent - should have a long hose connected that follows up and around the seat mount, open at the far end.
Any chance you got the jets re-installed in the wrong locations (mains or air jets), since some are different between left and right?
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'04 Suzuki LTZ400
'16 RZR XP4 1000 Turbo