The issue is resolved, I think. Long description of what measurements I took and what the parameter changes were for anyone that may be in a similar situation at any point. Digital cameras are nice, as I was able to take a shot of each measurement to reduce the risk of misreading. I will tack a couple samples to show the setups onto the post later if anyone cares.
Having nothing better to do today (that I wanted to do), I spent way too much time quantifying the travel for all three axes. I would put more weight into the results if I had done this when I got the machine, before the wear in the leadscrews, but I found interesting results.
The equipment was a heavy surface gauge base, Noga arm, and Mahr 810 (near) constant force 40mm travel (0.01mm resolution, 0.003mm repeatability, 0.025mm max error over range, recently certified). The surface gauge was located on the bed by boring holes for the drop pins into the waste board and using spray adhesive (scotch super 77) to tie it down. About as rigid as it can get without boring and threading the bedplate for the indicator mount. I would have used the 125mm indicator (ya, I got some special measuring tools) for the X and Y axes so I could quantify from a single central reference position, except that it isn't in certification, and I would have needed to remove the cover as it is nearly 500mm long.
Alignment was referenced using the X and the Y guide rods, and was good enough that the indicator tip did not shift laterally during the measurements (close enough not to exceed the play in the spindle bushings for the indicator). It is about the end of the season where I can control the temp and humidity of the workspace, so I was at 23C, close enough to 20 not to need compensation. It is supposed to get hot and humid over the weekend, so that may take me out of range for some measurements until the fall.
Fired up PuTTY for communication with the controller, wrote down the original variable values, and went to town collecting data.
What I found was that the X axis leadscrew travel is (using factory setting of 200.0steps/mm) fairly uniformly 0.0047mm/mm low, with little variation over the entire length. This was measures by making 5mm travels to 35mm (to reduce risk of crashing the 40mm dial indicator) and recording the actual position relative to the starting point. Then, reposition the indicator for the next 35mm and do it again. And again. And again... Each segment was reversed in the same 5mm increments as a check, and the measurements matched within the measuring instrument spec throughout, indicating insignificant backlash in the leadscrew.
Since the X axis error was pretty much uniform over the screw and repeatable, I reset the steps/mm variable and reran the test. The error is now well within spec. I reran my gauge piece (the 70mm spaced holes) and the hole centers came in at 70.05mm, well within tolerance.
I did the same for the Y and Z axes. I figured the Z axis would have pretty significant non-uniform wear, and was not surprised. I was surprised by the Y axis, until I though about how I usually set up jobs. about 80mm of the leadscrew is all over the place (+/-0.05mm or more per 5mm travel), but the rest was a uniform 0.03mm/10mm as the X axis, so I reset the steps/mm to match and know where I have the highest accuracy. The Z axis was all over in the area that get the most use. I took a bunch of measurements (5mm increments), did some stats, and reset the Z axis as well.
Overall, not a major issue, and manageable. Just took time. I only ran a small segment of the X at 0.05mm increments (for 5mm) to look for cyclical errors. I didn't note any that weren't within the spec of the measuring tool (0.006mm hysteresis), so by Ockhams Razor will assume a lead error on the X axis screw, but not drunken threads. It is still as good (or better) than the leadscrews on some of the (new) manual mills I have used.
To get the new value for the steps/mm settings, I used (1-discrepancy)*current
For the X, the discrepency was -0.0047 (0.16 to 0.17mm short over 35mm) and the original steps/mm value was 200.000, so 1.0047*200.000--> 200.940 steps/mm.
Retesting gave about 0.01mm error over the 35mm travel, which is essentially nil (half of that is taken up by uncertainty in the measuring tool, and all of it is taken up by two of the nominal 0.005mm step of the machine) and well within spec for the machine. The Y and Z came in better than they were, as well, but due to the uneven wear, they are compromises. This does tell me that at some point in the future, I am investing in replacement leadscrews. Probably be a few years, though. It is no where near the limit yet.
All in all, an interesting endevour, and I have the first fixture I need done. The 70.00mm center-center came in at 70.05mm (+/-0.02 using a 50-75mm Mitutoyo micrometer), which is in tolerance, and, even better, allowed the dowel pins to slide right in to the microscope alignment holes. Figure a 0.01 or 0.02 runout and/or wander at the tool, and that would give this much error. Now, on to the other fixtures for the same microscope.