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The hardest thing about jetting the EX500 is getting the airbox back in when you're done.
and a K&N isn't necessary.
And the only reason why I'm not telling you to skip the exhaust is cuz it's a great deal from another forum member... these things don't respond to power mods like other bikes.... seriously. In fact, the further you go with the EX, the harder it is to get the tuning right. Go with pod filters and you're almost guaranteeing yourself some dyno time to get it dialed in & you'll still probably end up with flat spots in the mid range.
So in short, as far as power mods go:
Keep the stock airbox
Jet it
Exhaust if you want to
Don't go any further w/o consulting a serious EX500 guru.