Firstly, I'd remove the K&N and replace it with the OE filter. There's a strong body of evidence that suggests that K&N's don't provide sufficient filtration.
I also suspect that given what you've done to the intake and exhaust, you've taken the fuelling outside the parameters that the ECU map will accommodate and the engine is running too lean. Time to fit a Power Commander or similar device to remap the fuelling. Throw in a dyno session for best results....call it £500 all in.