AJ, that is quit a document you put together on your build! Do you want to come put one together for me? LOL Your build has some similarities to mine with the inverted gear rack, gear reduction and spring loaded motor/gear mounts. How is your optical height sensing working? All i use is a floating mount with spring return pressure and a microswitch that triggers when the torch tip hits the material, and then the program backs off the measured amount of offset.
For making sure THC is set proper, just make sure by close measuring and making sure it is repeatable that the torch is at the exact right cut height after referencing and going to cut height (.080 or .0625 for me depending on tip), and adjust the ipm to get just the right amount of laglines in the cut, read the dross to tell if you are fast or slow, and then start another cut and read the voltage it puts out when in the initial portion of the cut after stabilized, set the THC to those volts and turn it on, nothing hard or guessing, and it can be set a few volts different for different tips that are worn more or less.
I have been told by a local guy who works for a large company that has a 1/2 Million $ or more machine that my table (when im not squeezing the last bit of life from my consumables) that i have much better cut quality than they do, and they have gas assist industrial plasma, and i have a standard 60amp handtorch air plasma.
I have had some interest in the table, and i have debated making a kit for some people to put together themselves, as i probably could not be competitive with big companies building the whole thing, but could be with supply the engineered hard part and letting the fabricators do what they do and build the rest, run wires for the control box, etc, with my gained knowledge of what works and what doesn’t, proper give and take of accuracy and speed, motor power, power supply size, using the Ethernet smoothstepper to get away from the parallel port, what tolerances are important, and which ones are not so much as THC keeps the torch were it needs to be. Proper cable shielding, grounding, optical isolation, etc…the list goes on and on.
My design is a fairly simple one that is nice and compact with all working parts, switches, etc on the gantry so you just make it the width you want, and then make the table the length you want and it can be easily made larger if needed. This is my 2nd table, the first one was really crude with scavenged parts and it was used to make the money for the 2nd one. There are still things that i might do just a little different, but most of them have a reason why they were done that way.
Adding the downdraft ventilation was another one of those really glad that i did things that didn’t really take long and wasn’t too expensive. I used an old good sized squirrel cage fan so the motor doesn’t see excessive soot, and it can be blown out easily and actually REALLY SUCKS! In a good way that is. 
I may have to take some videos doing an overview of the table and control box, talking about some of the important parts in depth. I can spend some time doing this, but if i am going to take too long with it, i need to figure out how to be somewhat profitable with the time spent, as i have a family to support.
Sorry for the long post filled with excitement, reading your build log quickly, kind of gave me flash backs to the long journey of research, learning, and trial and error of building mine!
Brian