It never does...not quite right. What will help is if you remove the MAF meter from it's little mounting bracket, and let it float between the two pipes. The pipes are solid, so it doesn't really need to be mounted on that bracket anymore.
That being said, you realize the factory setup is a "cold air intake" right? You are essentially replacing the factory stuff for something that can actually hurt performance in some situations.
The bend in the pipe before the MAF can cause dead spots in air flow, causing your MAF to not operate like it should if those dead spots are in the meters path. IF you have some drivability problems after it's in, you might want to try clocking the MAF to make sure there is a steady stream of air hitting the meters sensor...