Seriously, grab the spindle and wiggle it. Anything that moves is a target for manual tuning.
Also, your cutters may not be perfectly sized. Instead of measuring the gap between the slots, measure from left-side-of-slot-A to left-side-of-slot-B so the size of the slot doesn’t matter.
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Cutters are fine, edge to edge is 1.73. Spindle flex is 0.002". Step distances are still well off from what I’d expect.
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