[Brian R.]

I don't see anything wrong in what you did. In draining and refilling the pan, you replaced about a third of the total fluid. If you intend to replace all the fluid, you will have to flush it through the transmission fluid cooler lines by the radiator (capacity is 6 qts). Your torque converter and valve body do not drain into the pan, but stay filled with the engine off. The differential fluid looks much cleaner because it stays much cooler than the transmission fluid. Also, the clutches in the transmission wear some and the lining dust ends up in the ATF. The torque converter heats up the ATF in the transmission to the point where the transmission needs a separate cooler in the radiator. The differential is just a gear box.

Be sure and check the fluid level when it is hot (after running through all the gear positions) and the engine idling.

I consistently flush my transmission and replace the differential fluid every 30K.