Replacing the air box with the cone air filters

[DucHead]

Are you referring to something similar to this? http://cgi.ebay.com/Ducati-916-748-996-throttle-intake-velocity-stacks-x2_W0QQitemZ370279132610QQcmdZViewItemQQptZUK_Motorcycle_Parts?hash=item56365b2dc2

Your throttle bodies are different than mine.  I don't think you need/can use the velocity stacks at all.  Just fit the filters to the tops of the intake hoses (part#4, Drawing 016, page 40 of the S2R parts manual), or purchase the TPO/DucShop kit.

Pompetta--- Did you notice the bike running rough and some what stuttering on acceleration? When I removed my breather and replaced with the TPO kit, I did not like the way she ran. Mine was all stock. I would really like to run the TPO filter kit, but I do not want to compromise performance.

I have the DP ECU, and the bike runs fine...plugs are light tan, no hesitation/stuttering.