I think you want separate switches for the home operation of Y and A. Depends on how rigid your system is, and how little noise you get, but generally, you home A separately from Y.
You can, if you want to, wire all the limit switches for X, Y and Z into one input, and even include the opposite (from home) A in that loop, and have one input for A, a total of 2 inputs on your BoB. A more conventional setup is 4 inputs, one each for X, Y, Z and A.
You really, really want to use shielded cable as Tweakie says. It used to be that the recommendation for shield grounding was one end only. Today, the recommendation is earth all metal really well and ground both ends of the shield.
Your basic wiring idea is sound. If you want to use 2 inputs, you can use a single conductor shielded cable running all the way around the machine, or you can use the 2 conductor shielded running per axis, and series them close to the BoB. If you use 4 inputs, then your basic idea works.
To put them in series, on the "near" switch, you cut one of the wires and put the switch on the two ends of, say, black, leaving the other intact and not connected. On the "far" switch you connect the two wires to the switch.
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