WOW!, what a thread
OP - you say you have CNC experience but do you have CNC machine building experience?? There is a world of difference here and from reading this thread it seems you do indeed know your CNC but not how to build one, just my presumption from the difficulties you are having with how the switches work. In a pre-built machine all this config work is done for you and the $$$$ go up, in DIY you do it yourself and the $$$$ stay down but you have to learn the intricacies of the system in use, think yourself lucky that the machine does use Mach3 and not one of the exotic flavours out there - Mach3 is probably the most flexible and easy to configure system going.
2 years ago I knew 100% of nothing about CNC, Mach3, G-Code or building a plasma cutter, 2 years later I have built two CNC tables and successfully made money out of both (for my own use). Yes I did struggle a lot at the start but the guys on here got me through.
You nailed it, I am a user, not a builder....(I believe I said that early on but anyways)....when I started out 15 years ago, I drew products in autocad, loaded them into an app that converted the drawings to gcode, loaded them into the CNC zeroed it, and ran the program....didn't have to worry about the estop, limit switches configuration nothing...
Then when I decided to get a cnc of my own, (cabinet maker) I looked into building and seeing as how it was WAY over my head, I looked at buying a complete system. I looked into $10,000 state of the art systems, outside my price. I saw systems for $1000, err no an idiot pays too much but a fool pays too little. Looked around for machines in the size I needed, found one, talked to the guy, watched videos and photos, and bought a turn key system...OOPSY no it wasn't .....nothing worked the way the 4 or 5 other machines I have used...
Spent 2 hours on the phone, it kind of worked, at least enough so that I could use it....and from then on, I worked around the issues..
The reason I am addressing this NOW is because I'm going to be replacing the BOGUS plastic structural parts with aluminum and replace all the BOGUS design flaws in the machine....Where I got screwed was in the photos and videos, the black parts looked like anodized aluminum....oopsy, no, they are NYLON and I can see the fricken gantry flexing when I run programs.....hell, 2 years ago I replaced, I ********* you not, the PLASTIC gear racks and pinions with STEEL....yes, that's right, PLASTIC gears....(don't laugh) but my 2 x 4 machine was slowly becoming a 2" x 4" machine because I kept breaking teeth.....
I thought I should get the software and electronics sorted before going ahead with the mechanical improvements....I'm doing this now because this is normally a very slow time for me and it took a beating before Christmas, I made about 6 months worth of business in 7 weeks.....