The issues are from the differential and the driveshafts, as was mentioned before. The 6R80 is probably one of the most dependable transmissions Ford has ever used and one of the best out of cars in general. I have 10k on mine and no problems.
I did have the drive shaft "clank" noise for the first few thousand miles but I actually haven't heard it for 4 months or so now. I'll be interested to see if it returns when the weather warms up.