Thanks man, it’s been a journey for sure!
I know I’m crazy as bat s*&. In the before time (right after High School) I started a tool and die apprenticeship, that was until Uncle Sam made other plans for me. Anyway I’m looking forward to making some molds and lots of other things.
Maybe I shouldn’t have made the post because we are in the end working with a “wood working tool.” My point is if the centerline of the spindle axis isn’t lined up with the Z linear rails things will never be the way “I” think they should be. Now at some point the Z axis needs to be aligned with the X and Y and there aren’t any provisions built into the machine to do that. At least not yet.
I hope someday I’ll be ask you guys, like what materials are you using for your molds and what feeds a speeds do you use? Keep up the great work.
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Uh, no. Not as crazy as the rest of us 
I just moved the spindle up a tad (thanks @djdelorie for the photos) so I will have to re-tram for the 3rd time this year.
But as you pointed out, some of us get too caught up in chasing perfect to enjoy what we do have. Which is kind of why we all went into CNC machines in the first place? Yes? We were in search of perfection…
Well, we got beyond humanly possible so now we grouse about things we can’t even see with the naked eye! 
I got new Mitutoyo 500-150-30 calipers today (with the data cable) and I mounted the tramming plate to the Z axis. When I did the bottom measurements across were 94.98 mm , 95.02 and 94.99. I then took out the precision stainless ruler I have and I could not see which one was which.
My first instinct is it wasn’t “perfect.” But them my old man kicked in and I remembered the saying, “Perfection is the enemy of Good Enough.”
Although for some of us, messing with the tools is the hobby 
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So I finally found time to do this, and sure enough, my entire Z axis is nodding forward 0.020" in 6" . The gantry rails (X) seem to be perpendicular to the spoilboard, but the gantry plate is not parallel to the rails.
I thought to check this because the spoilboard has noticable ripples in it 
So the question becomes: where to shim? I can think of three locations:
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between the gantry ends and the risers (fortunately, the nod seems to be the same whether the carriage is on the left or the right)
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between the linear bearings and the gantry plate
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Between the gantry plate and the Z ballscrew assembly
I suspect the spindle is also nodded relative to the Z ballscrew assembly, but the shimming options are suitably limited there. One step at a time 
I put the shim between the bottom edge of the spindle and the spindle mount because my spindle was nodding forward like yours.
Guess what, it wasn’t 
It turns out my framing square is off-square by about as much as my spindle was. YOU HAD ONE JOB, SQUARE! Spent most of a day disassembling, assembling, testing, disassembling…
Ended up with a 0.006" shim between the Z axis and the gantry plate, and another 0.006" shim between the Z axis and the spindle. I think I’ve got the spindle within 0.001" per 1" or square, and honestly, that’s closer than I should be caring about for something that cuts sheets of plywood
Now you have to engrave ‘NOT!’ on your square
Yes, but wasn’t it fun? OK not so much but now you know.
I blame all the 2 to 4 letter maladies they’ve come up with to describe why I am the way I am. ADD, AS, OCD but mostly BS. I’m glad I’m not trying to make a living at this. My machine is apart more than it’s together.
Framing squares are ok for construction, but usually not woodworking. I have a smaller precision square that I use as the reference for all my other squares, and I actually check them regularly because some of the adjustable ones move around, and if you drop one, that can mess it up. I think I went through 4 framing squares before I found one square enough to use to square my table saw crosscut slider.
The other problem with most framing squares is the edges are not flat and smooth (they are punched out of sheet metal, not machined) so running a dial indicator down them can be difficult.
To borrow a method from “leveling” cnc machines, the approach is to use machinist level (accurate to greater than 0.0002”/10”), to get the x and y linear rails level to gravity/earth. Once those are level with respect to earth/gravity datum, a granite surface plate can be shimmed to also be perfectly level to gravity/earth. From this granite surface plate, you can check perpendicularity of Z axis linear rails to both x-axis and y-axis by using a 2-4-6 block and an dial indicator while driving the spindle up and down indicating off the vertical face of the 2-4-6 block. After z-axis is perpendicular to x-axis and y-axis linear rails, then can tram the spindle to same surface plate.
Unfortunately Avid didn’t design in an ability to fine adjust anything besides the angle between the z-axis and the y-axis using the eccentric nut, on the spindle mounting plate. Adjusting the other 3 angles (1: z linear rail ⊥ to x-axis, 2: z linear rail ⊥ to y-axis, and 3: spindle ⊥ to x-axis) is up for the customer to figure out.
One can buy the machinist level, 2-4-6 block, and granite plate for $100 each on Amazon.