I always thought the catless up pipe was more of a safety mod on the 02-05 WRX models... I didn't think you needed a specific tune for it, although a pro-tune would help maximize the gains from it since it would allow the turbo to spool a little quicker. Please correct me if I'm wrong.
It would probably be a good idea to take a look around and see if you can spot any obvious points of contact around your exhaust because it can shift around a little when you start and/or rev your engine. The solution could be to get stiffer/longer mounts or bend the hangers slightly to allow a little more clearance if it's hitting anything. Put the car up in the air and gently wiggle the exhaust with your hands and see if it comes close to anything. Since you said you notice the sound coming from the passenger side near your turbo, you might want to check to make sure it's not hitting your turbo heat shield or anything around that area. Also, check to make sure all the bolts are tight.
07 WRX (Albins 5MT + Blouch 20G)
Jorge Carrillo Tuned (365 whp/340 wtq)