Just wanted to share some photos of how I protected my limit switches.
On the Z axis, I relocated the switch to the left side. I drilled a hole on the Z plate up through the makerslide slot. This allows the wires to be concealed in the slot on the makerslide. (The switch does not have to be relocated to the left side, I just chose to do this.)
In the photo above, my Z axis is all of the way up. Behind the limit switch you can see a bolt. This bolt will be explained later. But as you can see the switch is completely closed but not getting crushed.
In the two photos below, the bolts can be clearly seen. These bolts go down through the Z plate. Two locknuts are attached to the bottom. These bolts hold the acme lead screw bearing, they replace the short ones that came with the kit. The protruding bolts come in contact with the delrin nut. When contact is made the bolts stop the Z axis from traveling up
With this mod I do not have to worry about the spindle clearing the Z plate. But as can be seen in the next photo, the spindle will still clear the plate. I did not have to modify the router at all. Yes it was I tight fit getting it to seat into the spindle bracket but twisting it slightly solved that problem. I also added 6 washers, two on the delrin nut and one between the spindle mount and the spacer. The thickness of one washer gave me just enough extra clearance that the spindle no longer comes in contact with the Z plate even if the bolts are not used as stops.
For the X and Y axis, I placed a plastic spacer onto a M5 bolt. These plastic spacers were leftovers from a LCD wall mount kit. The spacer can be seen below.
On the back of the X carriage I had to drill a new hole for the upper bolt on the limit switch. By slightly moving the switch up, this allows the roller to roll across the top of the plastic spacer keeping it from getting stuck between the bolt and the switch. By having the roller roll up and out of the way, this allows the limit switch to close all of the way without getting crushed. The carriage actually just slightly protrudes pass the switch (in the closed position). This allows the plastic spacer to completely stop the carriage movement without crushing the switch, all of the force is directed onto the carriage.
The Y axis is similar to the X axis
Hopefully some of you find this info helpful and it keeps you from crushing your limit/homing switches