Good questions Adam.
Here's my take. If your turbo and converter combo have quick spool up, you might not see any ill effects of stepping up to 3" pipes at that levels. However, if your combo does not spool up super fast as it sits now, you might see some slight lag. (although some have reported zero difference) Lag created by having to fill up the larger 3" OD tubing. There was an thread either on this site, or another that discussed this very same topic. IMHO, if the converter / turbo combo is right, running 3" pipes would be a no brainer. Especially if you have a 3" t-body and or your turbos discharge takes a 3" hose. No more reducer hoses. The thinner walled 3" pipes that typically come with some ICs also dissipate heat faster than some of the older thick walled 2.5" tubing. Some of which were made out of SS and weighed a ton. I have seen many friends put a FM IC on with 3" pipes on mid to high 12 second cars and pick up quiet a bit, however, most of them already had higher stall converters on their cars to match the turbo they were upgrading too. A lot of things change when you throw big go fast parts on a combo. It's best to take it one part at a time, tune it the best you can and keep it simple. That is the direction I am currently taking with my current T. Simple. No more race car monster this, huge that, it's a very bad disease and spreads rather quickly.
The headers again come down to your converter. It has been proven time and again that if you do not have enough converter and try to run say ATR or Hooker headers, you will experience severe lag on a relatively stock motor. The Hooker headers were the worst of all due to the extremely long primary tubes and even longer up pipe to the turbo. I can only imagine the lag would be similar with the ATR headers on a low stall converter when running the T/As. But until someone actually logs some before and after data, this is only me speculating.
I would think if you want to run a 6131RE and T/A headers, and lets say you had a 9.5" converter that would flash stall to 3200, you would be fine and maintain relatively quick spool up, even with 3" IC pipes. It sure would help with getting the exhaust out that's for sure.
I'll have to keep searching for that post.
HTH
Patrick