Has anyone had any issues on an 05, or preferably 06, Mustang GT related to the electronic Throttle control?

I finally got my Mustang GT (yellow, manual, IUP, Shaker 500) last week Wednesday, and today the "yellow wrench" warning light came on. Owner's manual says it is a problem with the Electronic Throttle Control. I took it to the dealership, and they contacted F.C.S.D., who did not provide any help with the problem. They believe it is a problem with modules not communicating with each other, and want to replace the PCM.

Anyone with similar experience?

I have the codes from the car as well. (400 miles on the odo, and now it sits)

Thank you!