I had all the mods listed below, except I put my stock PCM back in when I go into the dealer for anything....
I even told them there was an issue with the steering... they ordered a new steering rack immediately, and installed it the next week, no issues, no questions, no squabbles. They also did an oil change at the same time, so they definitely saw the CAI (hard not to see), and probably the motor mounts, and the exhaust work.
The only thing I had to do was as I said, swap the PCM back to stock... I only did that because I can't afford it if they flash me back to stock.
Like the other guy said... if they have a ringer, and they are a real stickler, they can give you a hard time. Most dealers will be happy to see improvement mods, because they support the aftermarket. Hell, at my dealership, they give cost +10% for local CGP members.

Might just enquire about a GenV blower.....
IMHO, go with a 3.5" if you don't plan on doing any other mods... you'll be happy with the extra 20HP... and your face will go

when you feel the new rush.
Also, gut your stock airbox (go to town with a dremmel tool, and take out all the baffling and extra plastic inside the box. It's cheaper than a CAI, and will give you better airflow... also... it's unnoticeable.
After that, get a 3" DP, u-bend and res removal. Your car will sound like this afterwards:
http://www.clyke.com/monte/lav74-Exhaust-Oct03.wav
Your powertrain warranty cannot be voided by improving intake and exhaust airflow (not talking about internals)... it only makes it more efficient. Like someone said... they have to prove the mod you did caused the break.
Glad to see a fellow MCSS'er in the house... let me know if you have any questions!