There has been quite a few posts on limit switches - there is one just going on now.
Limit/home switches can be wired up any number of ways to suit you. Basically all the switch does is send a signal (on or off) to the computer. All can be configured in Config/Ports and Pins/Input. There are five input pins to your computer - 10 to 13 and 15. All these pins are internally connected to a pull up resistor in the computer - i.e. if they are not connected to anything, they show a 5v signal to the computer.
You can test this by going into config, setting the pins, and then switching the inputs to "active high" i.e. active low is off (red cross). This should, without any machine being connected to the computer, show the led on the Diagnostics page as lit.
It is normal to use the switches in "active high" mode. This is because any fault in the switch or wiring is then detectable, before any damage is caused to the machine.
To set up the switches, all you need to do is connect the limit/home switch to a 0v terminal (pins 18 to 25 are at 0v - although check on your computer if all are being used). Fasten the NORMALLY CLOSED output from the switch to one of the input pins. Set up the Config page with the pin as active high.
This means that the pin into the computer is held low (off) in normal use. The carriage comes along, hits the switch, which opens, cutting the 0v signal. The internal resistor pulls the input high, and the led lights.
You do not need to install everything on the mathe/mill before you try this, you can experiment on the workbench before installation and see how to set everything up. You will see that any bad switch, loose wiring etc will cause the input to activate - warning you of any trouble, before it happens.
You can repeat this with all the other switches. You do not need any complicated wiring from +5 to 0v or anything like that.
You can save input pins by wiring from 0v to Sw1 to Sw2 to Sw3 to an input pin (use the normally closed contacts again). This means that all your home switches and limit switches go into one pin. Mach3 can sort out which one it wants to use.
Home switches can double as limit switches - again Mach3 sorts it out.
Again - your Estop switch can be configured in either way - active low or active high - or you could include it in the daisy chain above.
Why bother with 5 volts - connect it via 0v as above.
The 3 axis ProboStep Kit - does it include a breakout board to make connection to
If so the instructions above should still hold good. The thing about Mach 3 is that is so configurable that a lot of the rigid wiring diagrams (whilst they would work) can be simplified. If you keep it simple, it is easier to use and troubleshoot.