I can see no issues tracing the wiring. However, there’s no continuity between THC Dir In and THC Dir Out and I suspect that is very normal.
You are correct. THC regens the signals, but there was one comment from @Dicky that said you MUST set the Stepping config to be negative pulses or the THC doesn’t work… I can’t confirm that it MUST be because I just followed his guidance on that and it worked. I think this is opposite of the original CF Mach 3 config.
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OK, so I got it all running. Tried to do the Z-calibration in Mach3 and I may have screwed-up somewhere, the Z now does not move ony makes a brief noise! Been screwing around trying to fix this for the last six hours to no avail! …and, I can’t get the motor tuning screen to open!
Any advice on this?
I’d go back to basics, disconnect the Z motor shaft from the screw shaft and jog Z to confirm that still works (I assume that you set your current settings on the driver to match your motor spec and you didn’t burn out a winding 
)
If that works, maybe you bent something in your Z carriage. Can you turn the screw by hand and does the carriage move?
Also make sure your limits flip the lights on the Mach3 diagnostics page.
YEE HAH!.
Ok, I reinstalled Mach3 amd all is seemingly good. Z-axis is calibrated! Limits are good, homing is good.
Where do we go from here Tom?
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Hmmm, Does the Z home at the top or the bottom. Seems like if it homes at the bottom limit sw, the torch will poke into the material. I’m homing at the top for now
Home at the top. That establishes the top limit and you can use G28.1 to home Z. The Mach 3 settings should initialize the Z value to something approximate to the gap between the top of the slats and the bottom of the torch. Also, I found that checking (or unchecking, I forget which) the control that prevents rapids on G28.1 moves keeps things a bit more civilized if you manage to lose your Z reference (it’s been known to happen). If you don’t do this the Z may try to slam into the top of the travel (DAMHIKT!)
The Floating Z switch becomes your ‘Probe’ signal for your M31 command.
One thing you need to know is how your Z step per unit compares with your X & Y values (which should be approximately 12800). In my case the Z step per unit was about 1/3 that of X & Y and, consequently, I had to downscale ‘V’ parameter in the THC by a factor of 3 (30->10).
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Ok, A swim in the pool and a couple beers and I should be able to wrap my brain around all that. 
Config->Motor Home/Soft Limits Z HomeOffset
Config->Ports & Pins->MillOptions THC Options check ‘G28.1 No Initial Move’
This says use slow travel for the entire G28.1 calibration cycle.
I leave the rest of the THC options unchecked (I don’t use Mach 3 to manage THC)
Config->SafeZ setup: Check Allow SafeZ moves, Check SafeZ DRO is in Machine coordinates, Set SafeZ to a reasonable value (gap above your work), Check Goto SafeZ when Stop button is pressed.
That’s pretty much it for my settings.
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Ok, will plug those in and report back. Also now may be a good time to get to readin’ that THC3T manual 
GREAT! …so, everything seems to be fine so far. I guess in SheetCam, I will now have to use Mach3 Plasma THC with Scriber and Backlash Compensation" as my post processor? …any pitfalls/configurations to lookout for?
That was three long days of work. Had some intermittent issues with db9 connections that ran me in circles for hours, but all seems good now. Will wait for the machine torch to get here before I do much more on this. (Pardon the Rat’s-ass DB9 Extension on the Y-axis, it works, but got the real McCoy on order)
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My single Z-Axis DB-9 umbilical :
pin function
1 +24V (fused at 1A) {may be used at later date to power proximity sensors}
2 Ground
3 Limit Switch Loop
4 Probe
5 NC
6, 7, 8, 9 Z-Axis Stepper Motor
Shield [grounded at control cabinet end only]
Suddenly I’ve got a problem. When we hit an M05 in the code, the machine stops, “DWELL” comes on, and a timer starts counting up. I cloned the original Langmuir profile, named it THC and did the modifications to the THC profile only. This dwell thing is happening when using either profile. what did I mess up?
Something is messed up in the profile because you’re showing 4 axis on the screen.
I see it, it’s actually the next line, G4 P500. I’ll wager your Dwell resolution been reset to seconds…
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Arrrrrrgh! …silly me!
Thanks much again Tom!! 
New BIG PROBLEM.
Tried to do a cut (THC bypassed) did a dry run, that worked fine.
Turned on the plasma and once the torch was lit, all movement froze and the torch stayed on, turnoff the plasma and immediately movement resumed. At least the E-STOP mushroom works fine!
Completely removed the z-umbilical and no change!
Looks like I need a shielded cabinet!
Makeshift Shield (wife not impressed) and grounded backplate to the Crossfire frame did nothing to improve the situation. 
The only thing you should have connected to your Controller Card’s ground at this point is the USB port. I’d buzz that out as it is a likely candidate. Note that that 5V supply (from the USB) does power the X & Y steppers so you’ll probably measure some continuity on the Step, Dir, and 5V pins.
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The 5V supply shares ground with the 24V in this PS. The 36V ground is isolated from the 5/24V ground. So, as much as i hate the idea, I’m thinking to remove the 5V and its ground from the controller, pop the little SMT diode back in there and power the controller from the USB. Or better yet, fit a completely separate and isolated 5V supply for the controller, maybe a buck converter from the 24V supply.