In the mean time you could try and see if you get a better result by pulling the x-rail all the way up.
That should also give you a more or less repeatable way of aligning them, just not guaranteed to be parallel with with the y-axis plane.
I donāt know if they already asked you to validate if they travel at the same speed? There was an issue with the quality of the lead screws at some point. (which resulted in clunking noises)
Obviously, something similar could happen on the z-axis. You could try to validate this and possibly swap linear modules around to make sure you have matching pairs.
No clunks. In fact 3D printing is real smooth, but assume due to the auto levelling.
I already had a different linear module replaced as it vibrated. So wondering if there is a bad batch of these.
123 blocks come today hopefully, I will try that out, but not totally hopeful
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@WilliamBosacker having placed my machinistsā straight edge on the base i am unclear it is a flat and consistently level surface with maybe the exception of the (milled? cast?) areas the linear modules fit in?
I ask because each of my y axis carriage mounts when measured from the print head using a dial meter are 100% level. But my straight edge show that across the regular portions of the bed it is not levelā¦ I note you put your red things on the base, does this mean (at least on your unit) you are happy the āunusedā areas of base are level?
Also those are terrible squares - they are red, so i bought the blue ones for $0.90 more 
I would agree with that, thatās why I used the extrusion of the Y modules. My base is also warped and distorted.
Edit: could be the Z towers, but Iād think it would have to be visibly out of alignment for that to matter.
Is it possible you have 2 Z modules that have mismatched leadscrews? If you issue a 100mm movement does each tower move 100.00mm exactly? That was an issue for awhile, QA/QC issues at the subcomponent manufacturer (and then not verified at snapmaker, itās just qa qc issues teh whole way down)
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@brent113 oh, i have never made sure the Z modules are the same height 
never occured to me the bed could have them at different heights? Could that cause my 1.1mm drop to the left reported in the mesh?
(i think I finally proved last night that its not my y rails, my platform, my heatbed or build surface causing this)
A good point. I verified mine previously and would recommend others do as well. My towers were level and parallel, within what I would consider an acceptable tolerance:
I saw you? recommend loosening the bolts on the Z tower X-axis mounts for the first adjustment: I also agree with that, and also did that to relieve any residual strain. You should want any strain to be pulling it back into square instead of out.
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can either of you recommend the sort of digital angle finder on amazon that would be good enough for me (a mechanical dumbass) to use?
I have several.
In this case I used one like this: https://smile.amazon.com/GemRed-Digital-Finder-Protractor-Stainless/dp/B00W395R5E.
I also have these: https://smile.amazon.com/General-Tools-828-Digital-Protractor/dp/B00563TLSI, and Wixey Digital Angle Gauge Type 2 with Magnetic Base and Backlight: Amazon.com: Industrial & Scientific which are useful in frequent situations.