If you took off the coolant cap and had the cross-contaimination issue you would have noticed a nice strawberry shake substance attached to the cap. If you didn't then it is probably something else.It didn't even cross my mind to check the transmission fluid and I do not remember the color of the radiator fluid... When the dealer calls me back, I will be sure to mention that particular issue to them. If it is cross contamination, should I demand a new transmission?
I have to ask thou, after the "thud" were you able to accelerate to the station or did you have to push it?
I wonder if it is the rear diff or something along those lines?
If it is the trans, they will probably source a used one for you over re-building since it may cost less for them to get a used unit.