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I have a 2004 400ex when I bought it it had bent valves I replaced valves got it running then noticed the timing chain slapping and about to break but other than that it ran fine. I got new sprockets new oil pump gear and new chain and guides. I installed everything out it back together and it back fires through the carb at a fast idle but doesn't do it when the choke is on. I've messed with the timing a carb settings for weeks and can't seem to get it right. The notches on the cam sprocket are level with the head on the intake and exaughst side at tdc. I set the fuel screw at 2.5 turns out from slightly seated. And put a new ngk Dpr8z plug in it and still it's spitting out the intake. I've also moved the chain a tooth back and a tooth forward just to see and it didn't change anything not better or worse. And the valve lash is set at .004 on intake and .005 on exaughst. Any insight would be much appreciated.
 

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Coughing through the carb is a sign of lean pilot or mixture screw setting. Have you done anything with cleaning the carb? Most likely the mixture screw tip is dirty and not letting it get enough fuel at idle. Is the quad bone stock with stock jetting?
 

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Back the fuel screw out 1/4 turn and replace the 38 slow jet with a 42
 
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