Setting up limit switches and a bunch of other things

Okay, brand new to LinuxCNC.  I have built a few 3D printers running Marlin. I am running 2.8.0 on an old Dell using it's serial port to connect to a C10 breakout board from CNC4PC.  www.cnc4pc.com/c10-bi-directional-parall...-interface-card.html .

I am using standard mechanical limit switches. www.cnc4pc.com/pub/media/productattachments/files/WS_229.pdf

The physical ESTOP switch does not work wired up like that. For starters the stepconf wizard will only let me label it an ESTOP IN, and simply won't recognize the second wire when plugged in as pictured.  When I move the wire to Pin 1 where I can assign it ESTOP OUT, or reverse them, or invert them - in any combination - I either get an ESTOP that I can't turn on or that I can't turn off. So I've unplugged it completely for now and am just using F1 on the keyboard. I haven't tried the lower "ESTOP as Hardware Disable" setup pictured here, but plan to when I get the limit switches going and suspect it will work. : www.cnc4pc.com/pub/media/productattachments/files/WS_239.pdf

When I run the Z home the Z carriage goes up very slowly, hits the switch, and just keeps trying to go up until I hit the ESTOP/F1 in the gui(gmoccapy). I'm fine with the speed for homing, but why is the signal not triggering the carriage to stop? I have to assign each limit switch HOME X, HOME Y, etc to avoid an error code - anything else and I can't even get the jog controls because an error greys them out. 

I am also trying to hook op an OpenBuilds XYZ probe, and I think it's not working for the same or similar reason - my own inexperience.  I've tried assigning this one to PROBE, All HOME, All Limits, and I think a few others and I just get a whole lotta nothing happening. The blue signal wire is plugged into pin 11, and the black is plugged into a free COM next to pin 9. The lights on the probe fire up because it's getting 5v.  docs.openbuilds.com/doku.php?id=docs:xyzprobe:wiringgeneric

I also can't get the machine to allow me to select a tool. I suspect that's because I can't get it to home.

I also have the router connected to an IOT Relay running into the OUTPUT pin 17+GRND on the board and it seems to be working.  I have to wait until the system is completely powered up to hit the power switch on the relay or it will just start up the router and keep going.  However if I wait to hit the physical switch until I have gmoccapy fired up I can turn the router on and off with the onscreen button in gmoccapy until I'm I'm blue in the face with no issues. 

I know that's a whole lot to unpack, what am I missing here? I'm not trying to dial in the machine yet, just trying to get to the point I can run some basic gcode spit out by FreeCAD.

Going by the diagram Pin 10 is your ESTOP in.
The pin next to Pin 10 is the common.

ESTOP switches are usually normally closed, so if the switch fails of a wire comes loose your machine will go into an ESTOP condition.

Your Pin1 is an output, so I can't really understand why that would be part of your ESTOP circuit. Unless you are using it to connect to an indicator lamp or relay.

Now your PDF shows 2 examples of connecting an ESTOP, one where the EN Pin is shorted to 5v and the other where the EN Pin is electrically shorted to Pin 10. Which diagram are you using for your wiring ?

So for the moment I think we should concentrate on your ESTOP issue.

If you could be so kind as to attach your ini and hal files that would be great.
the location of these files, in case you are not aware are:
/home/yourusername/linuxcnc/configs/nameofyourconfig/

I think these are the files you are talking about.  

EDIT:
I tried the alternate wiring suggested in the PDF and it did not work.  So ripped it back out. Keyboard ESTOP is working just fine. I have better things to do than screw with a nice-to-have.

Pressing F5 starts up MDI, but then trying to home Z just causes a crash.If I can't home the system I can't load a tool.  Although I just officially tested the jogging controls with a tool running and I can manually cut plywood with the jog controls.

EDIT: 
Been reading this thread: forum.linuxcnc.org/49-basic-configuratio...roblem-homing-z-axis

Should I add "HOME_IGNORE_LIMITS = NO" to the ini(obviously without the quotes)?

EDIT:
This is the ESTOP and the limit switches I am attempting to use.  www.amazon.com/Emergency-Stop-Limited-Mi...f_=pd_bap_d_rp_186_t

I don't see a single thing about running them off of 5v.

EDIT :

Had an idea.  Switched the limit switch wires from NC to NO, took off the inverts, and changed "Home [axis}" to "limit [Axis}". GMOCCAPY started up with no errors. The limit switches now deaden the machine when tripped, I had to reverse the Z wire back to NC jog the axis down while holding it closed, and then change it back to NO. I jogged the machine into a corner on axis almost touching all three switches and hit the home which zeroed the DRO indicated by it turning green and only displaying zeroes. Suddenly the tool change was available. I had set the XYZ probe to "Probe In" and so I decided to try it with a bit in the router. I jogged it down to the probe and got the message that the probe had been tripped. So I guess I have to figure out a program to have the machine do that automatically? Touch off is still grayed out, something about offsets, so I guess I have to figure out what that means.

I have a feeling the machine is basically running now.  It's just a matter of familiarization, not mechanical or something set wrong. Thank you for the replies.  

Crash as in the the carriage hits the limit switch and then the end of travel and the motor keeps turning as though it never closed the limit switch. I haven't tried setting the switches to "Home [axis]" since switching the wires over to NO. Not all of them, I tried just homing Z. 

And yes, Z0 is at the top.

But no, as of yet the machine has not performed a successful autohome, but I can zero out all of the axises manually if I set them all as "limits" in stepconf. Then manually jogging the router down to the touch probe I was able to verify that it is working because as soon as the bit got to the touch pad I got a message where the error messages pop up. But when I jogged the Z all the way up closing the limit switch, and the program ESTOPed no longer allowing me to turn the virtual power switch on to use the jog controls, so I had to stop, pull the wire, plug it in so that the switch was now configured for NC, hold it closed, jog the z back down, and then reconfigure the switch for NO.

You have alot going on there. You cant do everything at once and expect to have good results.

Split it up into logical steps. example: Inputs and outputs.

Check your inputs. I would start by connecting back the estop and get that working. That is one of the basic things that you need to understand or you will just be going in circles. It is not normal that it doesn't work.

Connect your estop input back up. Then go into the menu Machine/Show Hal Configuration then go into Pins and drill down until you get to your input. click Watch then click on your estop input number. It will show up on the right as a yellow or red circle. Toggle your estop. The color should change. If that is working leave it connected because the probable error is in your hal. If it works then open your hal and comment out the following: like below:#net estop-out <= iocontrol.0.user-enable-out
#net estop-out => iocontrol.0.emc-enable-in

Put this:

WTF? What is wrong with the code and spoiler tags. It is hosed.

Those files are auto-generated. How are there sections that just missing?