I just did mine last week. I really wasn't sold on how much I would gain from a complete headswap vs a better flowing intake. For 260 bucks, give or take a few, you can get a complete swap kit and RTV the intake to the stock heads as some have done. I went a step further and bought adapter plates for $112 to attach my intake to the stock heads. Both methods seem to be good but I just wanted the extra knowledge of having a little better flow from the PI intake to NPI heads.
Now by air intake and manifold I believe what you are refering to are one and the same. It is not two different items unless you are meaning something different than a lower intake manifold.