So the machine is back together and apparently working. I did a dry run on paper of a spline that I cut several years ago and it seems ok. However there are still a few little niggling things that I need to sort before this project is put to bed.
Firstly, when I tried the flushing water having got things back together, the machine made a big puddle of water

Now this is coming from under the main body of the machine, and there is very little plumbing in this bit - most is in the main water tank. It will be something trivial but I'll have to take off a few panels to see what. Basically, pressurised de-ionised water is fed to the two 'flow control valves' below the plotting table, and from there is routed to the upper and lower flushing nozzles. Water then drains out of the big casting that is the work support via a flexy pipe back to the tank.
Secondly, when the machine was delivered years ago, one of the two sliding guards that move around as the work table moves was missing. As they are supposed to be bolted together to form a rectangle with a large square hole in the middle, half of one isn't much use! So I never fitted them - I did however order up a sheet of 2 mm aluminium to make one. The machine body has a 'kerb' of 8 mm x 10 mm aluminium bar that catches on the lip of the covers and limits their motion. One had apparently been forcibly ripped off as it's remains were still attached - I've never made the covers as I didn't have the bar !!!! Bar stock on order

Thirdly, the upper wire guide assembly racks up and down like the Z axis of a mill, the idea being to minimise wire length and water flushing distance for thinner work pieces. To this end the cooling and flushing pipes and power leads have sufficient free length to allow the downwards movement, but they flap about and get tangled in the polycarbonate anti-splash shields - so they need some form of re-routing or maybe just tidying up
Fourthly, having just re-threaded the wire I am even more convinced that the 'Vee Ditch' wire guides are the way to go, although it will need a bit of ingenuity to fit them and construct suitable flushing nozzles I'm sure it will be worth it!