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2005 Yamaha Kodiak 400 ultramatic. The bike will start and run for bout 3 seconds with no choke applied (cold 25c outside temp).) Then it starts to run rough and die (to much fuel?). Feathering the throttle doesn't keep it running. So try the choke. Just a little choke will help it run for bout 10 sec then it seems too flood itself(I think). So I apply Max choke and eventually it will start. I leave the choke on near full untill it warms up and the bike runs fine . I checked the fuel filter, petcock, air filter, fuel lines, The plug has good gap and dry and all seem fine. So I think its getting to much gas perhaps the Choke IM not sure how to adjust the choke. So any Ideas Thank you.

UP DATE: After riding for an hr. The bike started running rough and dies I let it sit for 10 min tried to start with no choke and would not start applied lots of choke it started and ran fine for the rest of the ride.
 

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With it starting and running with the choke on you are getting too much air and not enough gas. With the choke closed you are limiting the air to the carburetor and giving it a richer air/fuel mix.

Your carburetor may need to be rebuilt or adjusted. You might search online to see if you can find a repair manual that will tell you how to do this. I might have a manual that will tell how to do it but I'll have to look for it. There is no adjustment on the choke other than how much you apply.
 

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Here is what to check for hard starting. This is for a 2000 but yours should be similar.
 

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