I've got the Ness stage 1 and it came with the high quality K&N filter that you clean and re-oil. I like it.
I then got a new cover from Kuryakyn to finish it off. I was going to go with the smaller round cover, but didn't like that you can see the wiring harness going into the TB area (not like a carbed bike for sure). Kuryakyn now produces a nice chrome cover for that wiring harness now, but too late for me.