If you're going to do a tune it probably doesn't hurt to go a little bigger on the turbo. Really, it depends on what your goals/budget are - is this a daily driver or for other purposes? Are you hauling a trailer or heavy loads? There are certain limits with increasing HP on the 5EAT vice a MT. There are some mods available for the 5EAT for your model year that can help (search for Transgo kit). I think it's good for the 05-07 MYs.I planned to check the turbo and banjo bolt when I do the up pipe and everything else. If the turbo is bad is it better to just go a little bigger or stick with a stock size turbo?
I'm actually in a similar situation and looking to replace the turbo. I have an '08 so there's no 5EAT mod available that I'm aware of - so any of my upgrades won't be too crazy. Some people like the BNRs, they have a good website explaining the different models. Some people replace the turbine of their existing turbo (there's some caveats for that option). Some people just get a stock replacement. Again it depends on your goals and budget.
I would agree with @Max Capacity that you might as well upgrade the DP while your doing everything else. Depending on your area, you might find someone selling parts on the Legacy GT forum.
Definitely sit down and read through the different msg boards - this thread is great, LegacyGT has a lot of info, and the forums on NASIOC are informative.
Outside of mods, make sure you're keeping up with maintenance.