I can tell you for a fact that a drop-in K&N panel filter will work better on a Mass-Air controlled Fox than a cone filter under the hood. The turbulance from the fan screws with the MAF sensor's readings and makes it lurch a bit at low speeds and idle, and you're just sucking hot air from underhood, whereas the stock airbox pulls air from in the fender and the MAF is designed to work specifically with that airbox in front of it.
You could opt for a fenderwell-mounted cone filter, but don't expect any more gains, realistically, over a stock airbox w/K&N panel filter unless you've got one seriously built-up motor to really make use of it ... and even then, you run into issues with that elbow ahead of the MAF sometimes requiring you to "clock" (rotate) the MAF sensor so it doesn't get weird airflow readings.