1). This kit will work with the factory exhaust. This package will work with an electric exhaust cutout, as long as it's post-cat for sound gains. If your cutout is pre-cat, then you'd really need tunes for both normal operation and the cat-delete operation. Your best bet would be to call us directly at 623-434-5277 so we can get more specific about your exhaust setup. 2). The filter included with the custom aFe intake in this kit has a dry, reusable media. 3). The Bully Dog BDX is a handheld tuner, though its screen is large enough to make it an adequate monitor when paired with its separate windshield mount.