I'll be ordering a downpipe this week and thn switching to the stage 2 map
It sounds like you are like me and you are thinking that you want the most bang for your buck, and if you are going to get a map, you want to get the most out of it. I don't have your car, but I did invest in the cobb AP so that I could mod it safely without going to a tuner. Cobb worked fine. After some back and forth between Bill (from Cobb via Nasioc) and my data logs, I was always under-boosting a little bit. Like drvsdwz said, I was ok because I would rather be underboosting than over boosting in terms of longevity of motor... At the same time, I was thinking that I ought to get the most of the car with the tune. After about 2yrs, I decided to go with e-tune solution. The main reason I went that route is because it was cheaper (distance to and from my house, and less expensive than the actual pro-tune) and offered me a solution that was more 'tailored' to my car. I went with Eric at torqueperformance and I am very happy with the results. He sent me a map, I data loggged, he changed some parameters, I datalogged with new map, and we were set! He even gave me a map for 91 octane gas (I was on 93 until very recently) at no extra charge.
Given that you are going with stage 2 soon, you may want to consider going that route. It seems that you may get better results because Eric can modify the map in order to get the most out of your mods. Now don't give me wrong, I think that going pro-tune is probably the most efficient way of tuning your car with your mods, but if that is not an option because of distance/price, than an e-tune is your second best (over the shelf cobb maps is probably the third best option in that order).
Just my 0.2 cents given your experience so far and the fact that you are thinking of going stage2 soon. You can always contact Eric and ask if he does maps for legacy's (I don't even know if TorquePerformance does GT's, but you get the idea about e-tunes).
Good luck, keep us posted on decisions/results!