My guess would be that the standard set-up is supplying very little air into your motor with the DNA stage 2 fitted. Pull the snorkel out and block the opening off to see if there is any change. I pulled mine at the weekend and it comes out without any hassles. I personally wouldn't remove the stock filter just in case your blocking of the snorkel opening failed.

I'm going with snorkel out and a K&N filter, but I feel this is not as open as your set-up

OX.........