The stacks work just fine with a black stain on them, no need to make it clean and shiny. Heavy residues can sometimes be removed with solvent, but I have had to actually use sandpaper to remove heavy char. It doesn't have to be inert at the end, it just has to cool the fluid and create a reflux to make vacuum.
The fluid is a glycol, so the acetone works better than MeCl2, I have also used methanol to help remove the oil. But when just changing the oil it is ok to leave a little residue in it. It also takes almost two bottles of fluid to fill it up.
When putting the stack back together, I just make sure that the side with the hole faces the rough pump connector. There is also a U shaped notch in the bottom piece that sits across the heater rod, but that is pretty obvious but if backwards it will put the hole in the stack 180 degrees off from the rough pump port.