Have a k&n filter in my f3. Never gave any problems from the second I dropped it in. But my f3 isn't stock.

A k&n filter is gonna change your af mix. Dunno how much but it does. If your bike is already on the edge due to Carb, fuel or air issues I can see it pushing your bike over the edge. Except maybe in IDoDirt's case. His and his wife's bikes are so pristine they prolly react to smog days

 

Ok so I threw in the stock jets, 135 on 1 and 4 and 138 on 2 and 3. I also put on the stock air box and stock filter. Still the same ****. Something else has to be wrong. Could the other jets in there have an effect? Te bike is fine in first gear it rips right up nice and smooth, then second gear about halfway through the rpms it starts to studder and i have to back off the throttle. Third gear, forget about it it just bogs down.
What could it be?