First off welcome to the forum! So, the exhaust system draws alot of heat, and therefore makes the metal look like"rust". You will not have to worry about it.
Thr whine is normal on all Expeditions. The clunks are also sadly normal and all our vehicles with Fords 10 speed do that, I think it doesn't have time to think and changes gears at the last moment and ends up shoving the tranny into a gear. That won't hurt it will just make it a not so great shift.
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