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I have never had a problem with mine. You might try a simple fix; disconnect the negative battery lead, wait a few minutes and then re-connect. Gives the PCM time to "forget." Then drive it for a 30 miles or so and see if that helps. Also check to see if all the air bridge connections are tight. :)
Do you have a hole directly under the filter in the shroud? That can cause a surge at certain rpm ranges. I had it when I had a conical filter in place of the stock air box and when I first put in the Blackwing. In both cases, I had experimented with a hole under the filters. It did not work in each case and I plugged up the hole. No more surging.
I have a large hole cut under my blackwing and it surged a little when i first installed mine. It would only do this at very light throttle positions/decel. It seems to have worked itself out in the few hundred miles since.
I have surging also, but only when it's cold. I think the air/fuel ratio is off. I've been thinking about cleaning the wires in the MAF to see if that helps. (Use denatured alcohol with qtips and be VERY gentle. Don't break the wires.)
Fill the hole up and the surging will go away. Been there and done that!
This reminds me of my early Mustang days when if you put an open element filter (say conical type) in the engine bay and did not shield it from the "prop" wash of the fan, you got a similar problem. The MAF sensor would get confused. I have my square hole in the shroud (my own surgery :D ) now filled up with a piece of black painted thin metal shim stock.
I have a Blackwing with the hole in the shroud and a cold air cover over it. I don't have any surging at all.
Do you still have the MAF screen installed? Because I took mine out like a dork and my car surged like crazy. I bought a stock MAF with the screen intacked, installed it and the surging dissapeared.
BTW, I did not notice any power difference with the screen in or out.