So. One of the issues with understanding all this stuff is that a CNC router or Mill with a movable head is way easier than a Knee Milling machine simply because as the head moves towards the table the distances get smaller so if we drill a 1" deep hole we go down 1"
With a knee mill if the knee is what moves (not the quill) then when we drill 1" hole we go up 1". My quill is always locked at fully up and only used for manual operations.
With my mill the home switch is with the knee all the way down. That's so when it heads to home we never have to worry about running into anything on the way home. And that home position is the machine co-ordinate 0.000. But we have no idea where the quill is. That we have to measure. But we don't know how long our touch probe is so how to measure the length of the tool sticking out of the spindle.
If we refer back to my original PDF drawing it's clear I have been able to measure this. It's not as hard as it might appear.
I started with the HOME command. Then moved the table up until a couple of stacked 1-2-3 blocks just slid under the spindle with a tad bit of friction. The readout from the LinuxCNC DRO (a negative number) minus the 4" of the 1-2-3 blocks gives the total knee travel; in my case 12.718".
Now that we have that value we can use the spindle to touch the tool setter and the PC DRO Z value plus a bit of math will tell us the exact position the switch closes which is 3.663".
Similarly now that we know the distance from the spindle to the table we can install the probe and touch the table. Again simple math will tell me that the probe switch closes at 4.784".
These 3 values: Total distance, Probe Length, Setter Height let me measure each TTS held tool or a drill bit placed into the Jacobs chuck.