Okay so when I was installing my BHR kit it I noticed my throttle body was filthy. I had read somewhere that you should not clean it with removing it because all that gunk get pushed down into the motor. So I am planning on removing it and cleaning it but I realized that even though I have a new motor they just put my IM with 95k plus back on the nice new clean motor. Should I remove that as well and clean it out?

Why not.

Would I need new gaskets if I remove it?

yes.

most likely the gasket is reusable, just dont rip it.

Are you talking about the Upper Intake Manifold or the Lower Intake Manifold?
I hope your talking about the upper. If you are talking about the upper, what gaskets? There is only o-rings.

nevermind ... since he is talking about his throttle body I think he is talking about upper ...

yeah the upper just has the orange O rings right? How hard is the lower to remove?

I just pulled a general P0447 CEL and when the dealership diagnosed it they came up with the purge valve on the upper extension intake manifold was clogged with crap that had accumulated in the upper IM over 90K+ miles on same. I asked if it could be cleaned and they said NO (more on this in a moment). So for about $800 I now have a new one installed - according to the dealer they said it had been redesigned since my 03 build 6speed came off the assembly line. Only outward thing I can see different is that one of the vacuum nipples is now capped off (the one on the bottom closest to the throttle body). This didn't look to be the case on my old unit (although I really can't remember for sure).

Back to the cleaning, I read on another site that one guy tried a bunch of things to clean an upper intake manifold and nothing worked. Then he stumbled across the 'secret sauce'. Easy-Off Oven Cleaner with Lye. Cap off one end of the upper IM with something that will not easily rot or melt from exposure to oven cleaner, fill the upper IM with the Easy-Off, wait 30 minutes, cleanse inside of upper IM with water, and PRESTO - your supposed to be good to go.

Man I wonder what oven cleaner will do to the plastic though?