If you do not like the SE paper filter you can buy K&N replacement filter which looks like the BIg Sucker Filter, I think the K&N part number is HD 0800 if I am not mistaken.
I looked into that kit and decided not to buy it cause it looks pretty close to the size height of the stock air filter in receiving air, unlike the Big Sucker air filter and SE filters.
I'd stay away from the SE filters. They have a tendency to fall apart and get sucked into the engine. If you do go with a SE Stage 1 kit, change out the filter to the K&N part number HD 0800. Much better quality. Also, they don't make a Ness Big Sucker that will fit the '06 yet. The size of the filter is irrelevant, it's the the free-breathing aspects and enlarged venturi that make the RK-3909 a much better choice than the stock unit.