The FLA-100 kit doesn't include limit switches, nor does it come with any suggestions on how to install them. I've seen a few different approaches online and I used those for ideas when I designed my own. I designed some custom mounts in Alibre Design PE and exported them to STL. The exports are attached below. Then I used the prototype of my CAM software to generate the gcode. I cut them out of 0.22" thick clear acrylic and then bolted them onto the machine (in some cases using 80/20 gussets for brackets).
The X-axis limit switches touch the bottom gantry extrusion, and the Y & Z axis limit switches touch the carriages. I designed each of the mounts to have a little bit of over-travel so that if the machine drifts past the actuation point it still won't contact the mount. The switches themselves I ordered from digikey. I botched the first order and ended up with a few really tiny switches that weren't really usable. Sometimes it's hard to visualize how it will all come together until you have the part in your hand.
The wiring was really straightforward. Since Mach3 allows you to share limit switches and home switches for all axes, I just wired all the limit switches in series using the normally closed connections. This means that Mach3 usually has no idea what caused the error, but all that matters to me is that the machine stops before any damage is done. During a home reference operation it only moves one axis at a time and is smart enough to be able to share the same input. So with just one input on the G540 I'm able to add limit and home switches the entire machine.
Once the limit switches were installed I ran the machine to its full extents to determine the soft limit settings. When the 4th axis is mounted on the machine I use a separate X soft limit to keep the gantry from running into the 4th axis frame.
Of course all of these precautions can't save you from a poorly written program (like the time that I dove into a workpiece way too quickly), so an E-stop button is extremely important. I mounted it on the frame near the corner where it could be accessed from just about any angle. I'm afraid to say that I've had to hit it quite a few times already. The model for the E-stop mount is also attached. The switch can be obtained fairly cheaply on ebay.