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Help with yz400f issue

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I have a 99 yz400f that I have owned for 8 or 9 years always ran great no issues other than general maintenance. I don't race, just trail ride a few times a year. Not as much as I would like. Last year it started to die when I came to a stop. It would idle fine just die when coming to a stop. This spring it would not start. I took the carb out and the needle and seat was tarnished (that nasty green shit) so I replaced it and the primary jet was plugged. Cleared that out and reassembled and now she fires up and runs okay but bogs at low rpm like it never used to and still dies when coming to a stop. The top end has never been gone through and she is stock other than a pipe as far as I know. I took all the jets out and cleaned the carb very well. Any suggestions will be greatly appreciated.

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Take everything back apart and get a new pilot jet, take some fishing line and fish it through all the jets and jet passages clean it really good and try again. What do you mean by primary jet??

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Primary jet, the smaller jet I used a tip cleaner for an oxy acetylene torch with carb cleaner and compressed air too clean it out. I have only rode it around the block a few times but it has never acted like this when I bring her out of winter hibernation. 

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