Interesting, would you put money on the K&N flowing less fuel? i had the head off the VVC for a rebuild and port clean up, on refitting i fitted a K&N and i was expecting the bike to need a main jet increase but i only found the needles needed a lift and the bike flowed the same jet at WOT settings. Same tuning that ive used on other 400's and got quite large increases in the main jet. I assumed the air box to be the main restriction and so never thought to try different filters.
May go back to the stock foam which actually covers a larger area than the K&N and retry.