We're all different here. A lot of folks are bone stock and want to keep it that way, and others want the max power and really don't care about warranty. But, the good thing around that is everyone benefits from that here. Which is the point of the forum.
My Duramax was "Emissions Deleted" and...
BD Diesel has released the Hi-Idle control module for the EcoDiesel!
http://www.dieselperformance.com/productManual/(I-00321)_1036620-27_High_Idle_Kit_GM_Dodge12.pdf
I've not come across anyone having transmission issues that I can remember. Hopefully it's a easy fix.. If you have any codes to read that might point us to some ideas, other than that we'll have to wait to see what the dealer says. Keep us updated!