The stock air filter will not fit under a round air cleaner cover. The SE filter is round and will fit. Also, the SE air cleaner comes with a different backing plate that attaches it your throttle body, but that also comes in the SE stage 1 kit. The stock SE air clenaer backer plate is raw aluminium in color so if you want to run the round nastolgic cover like the Evo's had then this would be fine, but if you want to run and open element like in my picture below, I would suggest you get the wrinkle black backer plate for the SE air cleaner. But heres a pic of my air cleaner with the Harley Davidson classic script.

Chris