what was the purpose for the pod filters? are you trying to get power? you can get more power with the airbox than you can with pod filters.
your valve train sounds horrible btw, especially for only 3k miles. which makes me think the jetting has been extremely lean, overheating the exhaust valves. or the guy you bought it from was a scam artist and the bike has more like 15k miles on it.
do a valve adjustment and check your cam chain to make sure its in spec. put the airbox back in. rejet.
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