Nice looking machine, Lance!
1. Are the cables shielded to the sensors? Are they sensing steel or aluminum? When you say they didn't work did you go past them and into the physical stop on the machine?
2. All I am using is sensors. Of course, there are hard mechanical stops (bumpers) if the sensors don't work.
3. I haven't watched the video you referenced. I squared mine by using a V-bit and cutting into the spoilboard at each corner for the largest rectangle I could fit on the machine (our machine is a 2x4) and then measuring the diagonals. I kept making adjustments until the diagonals were identical.
4. Mechanical click? Electrical? If you happen to shoot a video do it widescreen and post so we can see/hear it. With power off are you able to freely move the gantry along the Y axis?
That's all I have (for now).
David