Once you start changing the intake/headers/enhaust or others that causes a change to the engine power characteristics, a superchip is pretty worthless.
Superchip worthless after mods? On the contrary, it's the best point to get one. It must be calibrated to all of your mods, but it will gain HP and TQ. Eric Grammetbauer gained lots-o-HP-n-TQ when he had his tuned on the dyno on top of SHM headers and a few intake mods.