It's completely worthwhile to get it tuned even if the car may have been tuned before. My car was tuned with an AccessPort before I bought it, but as the AP was not with the car, even though I know it was still married to it, I used my AP to make sure I knew what tune was done to it. You can't just trust that someone was using a good map for the car, so until I can get it actually tuned, which I'm not really sure where to go in Utah now that Cobb is in AZ, I'm leaving on an off the shelf (OTS) map. At least that way I know what is happening and it's safe. With a TBE, it needs a tune, but Boosted09 is right that it would have a check engine light (CEL) if it didn't have a tune done (generally speaking. . .). Remember, a TBE is not the same as a Cat-Back (CBE). You'll actually see a different pipe right off the turbo under the hood. If it's a single, round pipe (it still LOOKS huge even so, but it's round) then it is stock. If it's a Bell shape or looks like there are 2 pipes coming off it, then it has a downpipe. If that pipe is still stock, it's not stage 2 and doesn't HAVE to have a tune. I hope that helps you.
Regarding the intake. SRIs are okay, it's the CAI that's not good on an 02-07. It has to do with the sharp bend coming from the fender creating turbulent air at the MAF sensor. Good luck, man.