So that nut was indeed loose. A few minutes with an allen key solved that problem, the z-axis is now locked. I suppose I should ensure that the brake disengages when 24V is applied before I go too much further there.
I can also confirm that the z-axis way covers are identical. The bottom one was a mess, chips on both sides. No evidence of chips on the ballscrew or rails though. Once I gave it a good clean with kero and an old toothbrush and removed the chip build-up from the inside of the folds, it concertinaed much better, although still not as good as the top cover, so i am swapping them.
I also found what might by evidence of a crash. Low on the front face of the left z-axis rail is what looks like a small gouge from a cutter. Both the running edges of the rail appear perfect, so I'll take a stone to that gouge just to ensure that it won't foul the carriage. The gouge corresponds to an aberration on the way cover. How a cutter gouged the rail without actually puncturing the cover is beyond me. I know that prior to rebuild the spindle suffered from high G vibrations, and crashes are a major cause of ceramic bearing failure, so it wouldn't surprise me.
That spindle rebuild could also explain the minor coolant loss. I'll extract a few cc from the chiller and confirm that it mixes with distilled water ok. The chiller only holds 2G, and can't be more than a pint or so low. I'll likely just top it with distilled water. Water soluble coolant is likely glycol based for both its anti-corrosion and anti-freeze properties, and should be tolerant of a few percent dilution.