If you have done everything correctly, and have no air leaks, it is most likely that you killed the low end because of the engine overworking to take in air as previously stated. I've done my own setup similar to what you have described, making a ram air setup into the stock air box, although my results were a bit different and the getup and go off the line was a tad bit worse but at speed, it was definately a lot better than stock although I burned through a half tank of gas after only 70 miles of some spirited interstate driving.
But think of it like this. You have a vacuum cleaner and w/ a short hose it has great suction. Same vaccum w/ a hose twice the length, the suction decreases and continues to do so as the hose gets longer. The engine is the same when it is starting from a stop. The shorter the intake tubing, the more air getting in. So the ram actually hurts the performance until you get up to speed enough for air to be forced in.