Well, I did the bypass about a month ago, but unfortunately, I was too late. I didn't notice anything in the small amount of fluid that came out during the procedure, however a couple weeks ago I started getting the occasional dreaded "rumble strip" shudder going from 4th to 5th gear at around 45 mph under light throttle.
Took it into the dealership, and they confirmed the cross contamination. Unfortunately, I have 105k miles on the truck, so I'm SOL with the extended warranty. I had them go ahead and flush both the radiator and transmission (w/ Amsoil), even though they didn't recommend doing either. Truck seems to be doing fine since then, but I know it's probably just a matter of time.
Has anyone saved a transmission after the cross contamination?
Bigger question...is there compatibility between different year models for the transmission? I know they are all RE5R05A, but would a tranny from a 2010 or 2011 function correctly in my 2006?