I don't use a G540 or a Smoothstepper (I use the parallel port).
All the limit switches can be wired to one pin, and so can all the homes.
You can actually wire everything to one pin, if you only home one axis at a time. The exception is if you need to home a slaved axis, where each side needs it's own pin.
If it were me, I'd get a cheap breakout board and use it for additional inputs like you're thinking.
If you want to use two machines, then they each should have their own electronics (including their own Smoothsteppers), unless you want to be constantly swapping wires around.