In response to question 1: i do not believe that the entire engine was repainted at the time that most of the modification, and lettering was done. i.e. the addition of steam domes, and the expansion of the coal bunker, as the Uintah made the changes not long after the #50's arrival. I've found no evidence that they changes the colors over the years, although the "aluminum" material may have been replaced with paint in later numbering schemes.
Question 4: There ar few photos that I've came across that are difiniteve one way or the other, but if you look at the bottom photo on page 94 of my book, you'll notice a distinct look of a flange on the middle driver of the front engine, just peaking out from the shadow to the left of the little pile of sand.
Question 5 : I believe that the Uintah used Link and Pin couplers, early on. I'm not familiar with coupler types, but evidence on early locomotive photos show them clearly, at least on the front.
Question 6 : I belive that both domes were "open" to the boiler going up and down the hill, and have never heard of any mechanism that they used to switch it.
I hope this helps??????
Rodger