In the order of crappiness, I think the headers take 1st. When I say headers, I'm talking about passenger side, uppipe, and downpipe. They all need to be upgraded to go fast.
The stock intake isn't "that" bad. I don't think you will pick up much with a ported intake and stock motor.
I believe a hotair will run 11s on the stock intake. I don't believe it will with the stock header system.
When a car picks up 6mph from headers, you know something is wrong with the factory design.