Ok, you removed the intake box from the throttle body. The intake you have has a 90 degree bend in it for the top mount throttle body correct? What is not lining up on it?

Trying to help, but hard to do over the internet with nothing to see.

I know the intake manifold topic didn't help, but after you put that cai on the small gain you will feel will fade fast. You will be looking for more. It happened to me.