How does it run under boost? Still rough? This time of year is when people really start getting problems with injectors. While you had the spark plugs out, did you compression test the cylinders? Some of what you're describing is eerily similar to my car as it has bad ringlands on cylinder #4. My car actually had weird performance at around 2500-3000 RPM. Why the larger intercooler with the stock turbo? You may need to tune for that, but I'm not positive that would make all that much of a difference with that intercooler. I wouldn't blame it too much on the intake just yet, but the Cobb and SPT intakes are good choices if you want to replace it with something other than factory original.
A quick and easy way to check the ringlands (which are a common failure point on 2.5L motors) is to open the oil filler neck when the car is already warmed up. If it's puffing smoke out the neck, it's likely that your ringlands are bad. I don't mean to make you freak out. . . I just wish I had known early on how serious my problem really was. I bought spark plugs, had the BCS replaced, took it to the dealer a few times, and got nothing for all the hard work, except time without the car.