Ok, cool, then its 99% a mechanical i.e. build problem. Forget about axis labelling it's irrelevant at this stage as you will need slaving on two axes but this is really simple - my breakout board can run two drives from each output as standard, not many can so that would work there.
Picture a bog standard x/x/z plasma table, then remove the frame between the two sides and chuck the torch out. make the side frames self supporting, I don't know if there is room to join them, maybe you need a crane or forklift to load the pipe?
So now we have two carriages running along two side frames on linear rail probably. On those carriages build another linear motion unit - a trapezoidal screw lifter would be good as it holds its position and does not self-drive from the weight on it, probably decent belt reduction from the stepper motor as speed is unimportant.
Now we have two points (the nuts on the trapezoidal screws) that can move in horizontal as well as vertical planes, separated by a distance that could theoretically be many metres, both these points will move in sync as they are both slaved.
Now we just need to bridge those points with a support, maybe a box section with triangulated support etc to keep it rigid and light, then fit some possibly nylon rack along it, build a carriage to hold the scanner, the traverse motor and coffee machine

then some type of cable manager under the rail and it will run up and down all day happy in the knowledge that both ends are perfectly in sync.
Is this a field or lab machine, as if field, dust and crud will need to be factored in.