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My thoughts, after sketching, is that if you placed the mill structure on the next tier up, it would yield a structure a bit taller than you desire. This being said, perhaps I should step back and discuss how mills are laid out. You may already be aware of this information, but I'll assume nothing for the sake of completeness.
Mills operate by using gravity to do most of the work, with hammers falling on the ore and the ore sliding down into the awaiting bins. With this being said, the hammers cannot be placed at the top of a tall structure, whereas they have to be on solid ground for obvious reasons. This combination of gravity operations and a preference for solid ground leads to our selection for the site of the mill itself, with many mills preferring sites with good stable terrain and good vertical separation at an elevation below the mine level and above the railroad grade level. This allows the operation to place the heavy hammers on solid ground in the upper buildings and then let gravity move the processed material to the awaiting bins below.
Hence, they would find a hillside and then carved terraced benches into it, each separated vertically by 20' or so - however much height is between the floors - and going only deep enough [10'-20'-30'] to place the equipment for that level. If you look at the Campbell Mill, you'll see that there is an ore cart in the upper left corner, where the ore comes in, but there is no delivery at the bottom, which would be fine for High grade High Value ore, but not a large operation like yours.
The building over the bins would be a sorting/grading/weighing facility, plus it may also house company offices for accounting and for managing mill operations. The smaller upper building may be a lft house or an engine house, or a receiver house where ore is received from a mill on the same elevation or higher up, or it may even be a small mill house, housing a stamp mill. The Campbell kit represents a millhouse with an upper receiver bin where raw ore is dumped right from a mine site.
Stacking them in this manner, with the railroad counting as tier zero, would put the bins at tier one and tier two [tier one is essentially "nonexistent"] and the sorting house is located on tier two. Next, we have tier three with the Muir Models upper structure or the base of the Campbell's Mill. Tier four and five would be contained by the back part of the Campbell kit [the roof extends out over tier four], whereas the hammers would be on tier four and the ore comes in on tier five.
Hence, I think you could place the mill in place of the upper Muir Models housing, thus connecting it to the lower sorting/grading structure and the storage bins below. That upper structure from the Muir kit could then be placed adjacent to the mill on the third bench for housing a boiler or an operations house with a boiler in close proximity, whereas this boiler would run the 10-stamp mill.
This overall structure would drive the height of your final hill, which may be more like a ridge line in at least one direction so you can model the ore line coming in on the fifth tier. You may even get in the mine head itself, but at this point space is indeed limited!!
Now I I do understand this final structure may be a large imposing piece, but I dare say this single mine is the driving force that built your railroad in the first place. The two railroads built to the Verde Valley[Jerome], the railroad built from Prescott to Mayer [which had lines running to Poland and all the way up to Crown King], and the line running up to Harshaw from Patagonia all followed this economic pattern.