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As for as I know Heidenhain LS403 is a 11uA signal . Not 1Vpp.
Please check the datasheet

Back to the 'knowledge well'... sigh.

What I CAN do:
I have my motion control working (I can job X, Y and Z in the correct directions - or at least in the directions I want them to move when pushing the +/- buttons).
     - I had to 'reverse' the homing direction of my X and Y axes in the INI file, changing the lines:
       HOME_SEARCH_VEL = -0.050000  ; changed 0.050000 to -0.050000
I have my spindle control working - I can turn the spindle on and off from the Axis UI
I have my home/limit switches working - I can 'home' my X & Y (I don't have Z-axis home/limit switches)
     - the 'home' symbol shows in the DRO section of the Axis UI

What I CANNOT do:
1) I cannot 'touch-off' any of my axes. I homed all axes, jog my router off of the Home position, click the 'Touch Off' button and leave the defaults as presented, click the 'OK' button and immediately get an error stating "Can't issue MDI command when not homed. This of course also translates to my MDI (F5) screen when I attempt to move the router around using the G0 command
     - I am somehow way out of 'scale' with motion - I was planning on using the MDI interface to specify G-Code moves and measure results. Of course I immediately got the "Can't issue MDI..." error so I returned to the 'Manual' tab to ensure I was homed... which I was.
     - At this point, 'eyeballing' alignment with marks on the wasteboard, a 5" move shows as ~1.25" on the DRO in the X dimension. I'm guessing Y will be the same - but Z will be different because it uses a different Acme threaded rod.

I did try to find a solution in the 1347 pages of the manual... but that document is just absolutely overwhelming. In fact - I tried going through it again, one more time before I pushed 'submit' on this post (I DID realize that at least part of my motion scaling issue is my INI configuration). I even read the 'history' this time and realized that LinuxCNC emerged from a NIST project that was based on Windows NT... if ONLY the guys that were first involved would have stayed there (insert joking face emoji here).

If you want me to repost this as a new thread with a new title - I am happy to do it.

Well that's frustrating -- found this thread, got excited, read it to the end, and... crickets. :-/

What happened?

I assume you can't just change the Z0 location as you need the Z/Y to be zero'ed with the 4th axis center of rotation.  Otherwise you could probe the top of the part stock and use "G10 L2 P1 Z0" to set a new Z0 offset.

If that's the case you can try putting a stock stop in your collet block.  The collet and nut will change Z-position when you tighten, but the part should remain (mostly) stationary... much like a lathe stock stop attached to the spindle (and not the collet).

Kind of a poor-man's dead-length collet system.

What kind of shaft couplers are you using, and how is (was) the motor connected/aligned to the ballscrew?