I set 1-2-3 blocks on top of the y-rails and then pushed the x-rail down on top of the blocks. This ensured that the x-rail was no more than 0.001in out of perpendicular from one side to the other. I can’t take credit for the idea though; it came from here…Carriage Tolerances - Unusable Over Distance >75mm From Center - #34 by brent113
I only use 1 block on each side instead of 2 like he did.
I still do this every few projects to reset it; I theorize that minute differences in the lead screws (steps, backlash, ect.) of the two z-rails cause them to become ever so slightly de-synced over time, and needing a reset. The MFG way of doing this tramming is to turn the machine power off, and then push the x-rail all the way to the top of the z-rails, making sure that each side is firmly against its physical stop. It’s actually pretty accurate that way, but twist in the base plate causing twist in the y-rails and causing the z-rails to not be perfectly parallel is where the discrepancy in that technique lies. Finding a way to secure the two z-rails parallel to each other would likely fix almost all of that.