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According to GSTwins.com or .org or whatever the GS500's are jetted very lean from the factory to begin with. Installation of a K&N filter can adversely affect on these bikes significantly. It is entirely possible that your jetting has fallen off the too lean end of the acceptable ratio. Along with the other suggestions given, try going back to the stock paper filter and track a few tanks.
Please report your findings so we can learn the effects of all your changes.
Also, the GS can stand taller gearing (like most bikes) for an additional gain. You should be able to go from the stock 15 tooth front to a 17 tooth front and see a good gain.
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