I guess the first question to be asked is if you are certain that you drained the transmission fluid versus the engine oil? Did the fluid also have a very strong odor? For transmission fluid to be that dark with only 60k miles on it, you definitely should plan to change the filter as well.
I'm not sure what you mean by filling the transmission and letting it run until cleaner fluid came out. Did you reinstall the drain plug, then run the engine and shift through the gears, then drain again?
-Rod