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Try adjusting the idle screw on the left side of the bike. You may be able to lower the idle there. As far as smoothing the idle out a bit, you may want to go into the map for the PCIII and add a bit of gas in the RPM section for the idle. This may help smooth things out a bit.

The biggest issue here, however, is that your recent modifications may have caused the bike's motor to be running overly lean. This can be dangerous and is the whole reason the PCIII is installed in the first place, so be careful. Ideally, you want the map tuned to whatever modifications you make, so that you can ensure that the bike isn't running lean and burning valves or pistons, etc.

Ray
 
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