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From CycleChaos

Almost every motorcycle engine starts better with a richer mixture when it is cold. This is due to the fact that gasoline turns into vapor easier at warmer temperatures. Less gasoline vapors can be counteracted by simply adding more raw gasoline. Chokes serve to enrichen the mixture by blocking air flow (some do add an extra fuel circuit though, especially on higher end engines). Once its warmed up if you leave the choke on too long you will flood the cylinders (time varies but you can hear how the engine is running to know when to remove choke). Some bikes never need to be choked at all it really just depends on you knowing what works best for your bike. Some only ever need half choke and would flood if you tried starting them with the choke fully engaged. The other side of having a rich mixture is having too little air. This could be caused by a clogged air filter, or more common on newish bikes an air filter that due to some circumstances (possibly trailering with the fuel on, also if say the bike had been turned over etc) has become soaked with fuel thus allowing less air in. A too-rich mixture (keep in mind that as it warms what is too-rich changes) will result in some fuel not becoming ignited and can result in a flooded condition where you have damp spark plugs. What you need is just the right mixture. Most motorcycles will need zero throttle when cranking and that is definitely the best way to approach a new bike. Some carbureted bikes do crank better with slight throttle, but these are rare cases. If you think you have flooded it hold the throttle wide full open to allow it to air out. Excessive flooding will require drying out the plugs.

The flip side of this issue is you are getting too little fuel (lean), in this case use the choke, make sure no gas lines are pinched, make sure vent tubes are clear, make sure air filter is secured. Loosen the carburetor drain screw and you may get rid of some water that might have accumulated, you could see it on what comes out as water will not mix with gas. Since your bike runs fine otherwise this is the less likely scenario.