I wouldn't say you need a new air filter but it certainly wouldn't hurt especially if you are already getting into the airbox mods to open it up and putting the exhaust on at the same time. An increased free-flowing intake will complement the increased free-flowing exhaust nicely...don't want to have one component restricting the gain benefits of the others.
I would recommend BMC filters, that is what I put on. Why? I dunno...its Italian? and is closely related to Ducati (made in Bologna).
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08 Hypermotard
05 CRF-450X Supermoto (CA plated)
01 YZ-426F