You don't "need" the jack - you could just use a pair of the 0.1" headers and a 2-way socket. But horses for courses.

You don't need independent X/Y/Z inputs - you could wire all microswitches, normally-closed contacts in series. Or, keep it simple and wire each pair for each axis in series.

I would recommend reading the Mach3 manual - it deals with this quite well. In particular read up on homing switches and soft-limits.