I ground off a lip on one of the edges on my K&N, it slips in fine now, but I always smear a layer of grease around that area to insure that it seals. So I'm not saying that's the way to go, but it was my route. I was pretty frustrated too. I never did like the 'plastic on plastic' seal of my K&Ns, so I always grease them anyway.
Having the scooter on the ground or side stand and and trying to put as much weight as you can on the rear of the scooter helps as it moves the air box away from the frame giving a bit more room, setting the rear suspension on the lowest setting helps to.
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