Taylor, this may be useless speculation, but I believe in one of our mutual freind's photo collection, there is a photo taken at Whitney of SVRy#2 pretty much wrecked out as a locomotive, with basically just the boiler which was used in later years to supply steam to operate a pump to fill the water tower. I am not certain if this was former Tonapah #2, or the earlier Brooks #2. Anyway, it could be the source of the stack.
Also, I believe the original mill at Whitney burned and the one there now is the 2nd one. I think you are right that the first mill was built real early when the tracks reached Whitney by Nibley and then later the replacment mill was OLC. I don't have my copy of R.S.&P here at work to check, but if you look I think this is mentioned there.
Wish I was there. Good luck with more exploration!