Just a comment on something I noticed the other day when this happened. I have a boost gauge and I noticed when it happened at a stop light that my boost gauge was showing zero instead of normal vaccum at idle. Don't know if that's the cause or result of the issue... bypass valve closing at idle? I may see if I can recreate the problem manually.

 

Mine use to have the rough idle before but it hasnt done it in awhile, and it also hasnt had the cold start problem(guessing they upgraded the software). I have an auto meter air/fuel ratio gauge in my car and it seemed the rough idle occured when the car leaned out real bad and taping the gas fixed it due to adding more fuel.