I just posted kinda on this subject under "The Clunk.........I had". You should read it.
As I'm reading the other posters replies to your questions I want to point out my experience with the Pro Cal tuner. Once removed I noticed better throttle response. My Son told me that the benefit with the tune is only about 3-4 hp and 8-9 pound feet of torque. You could feel the torgue at low end with the tune.
Now regarding a new tune. I have in the past gone with a custom tune from RET on my '06 Supercharged Saleen. Greg does a good job and will get it right if there is a problem free of charge.
My Son has done significant research on canned tunes. He is now convinced that AED is the one. He has emailed Sean ........in Shingle Springs CA who has responded quickly every time. A bit cheaper than the custom tune.
Oh yes, and the clunk. If you get a Pro Cal I can't say you'll get the clunk. I did.
I've heard but can't verify that the Pro Cal can reduce your engine warranty. Look into that. I'm not sure if your computer will tell the dealer that you have uploaded a tune even if you remove it from the car when taken to the dealer.