The supercharger is how air gets into the engine.
Two rotors force the air into the cylinder heads creating more pressure thus more horsepower.

Your engine is designed to run with the parts that are on it. If you change the intake manifold to one on a 3800 without a supercharger you will get into a situation where you will have to change the injectors and add other parts to make it run correctly. Not to mention the reprogramming issue.

If the supercharger is the problem try these people.

http://www.pse.us/indexpage.htm

I bought a s/c from them and it works better than the original.

He is right. but if u try the cheap way it does not turn out to be the cheap way you can get a computer for a non supercharged 3800 and an intake for it but you end up spending the same amount of money and loose a bunch of power