That is true. The 04 LS has a different intake manifold. The throttle body is located in the front, and is also 3-1/2in. rather than 3in. If you have the ability, or know someone who does, just fab your own.
As for the exhaust.. From the downpipe to the cats, the pipe is 2-1/2, after the cats it is reduced to 2-1/4. iv'e tried many different combinations. I started by leaving the factory resonators and running 2-1/4 strait back. Next i removed the resonators and did 2-1/2 cat back with super 40's (btw, the flowmasters sounded like crap on the LS, with a very loud resonance in the cabin around 40mph).
After these combinations i did the turbo...after blowing the turbo up and deciding to move its location, i fabbed a "temporary exhaust". I put a dual 2-1/2 to 3 collector and ran 3in back from the cats, single pipe, no mufflers. I surprisingly found this to be my favorite exhaust so far. It seems like it has the perfect amount of back pressure, i get great response with it. although it is rather loud, it has a great sound to it that you just cant get with duals on the LS (just a personal preference)
Within the next few weeks here, i am planning on putting together my new turbo system (ill try to post pics of the new parts soon.. i replaced the T4 .60 a/r compressor, .48 a/r turbine with a Super 70 trim .60 a/r T4...4inch inlet, 2-1/2 inch outlet... this will hopefully get rid or the low end lag i had). With the new set up i am planning on running single 3-1/2 back.