When aligning the shafts you have two primary considerations. The first is to have exactly the same center-to-center distance on the shafts as the z-axis block. Second, it should not change or fall out of adjustment easily (ideally, never).
The center-to-center problem is huge with a wood structure. You just can't hold the accuracy of the holes required and even if you did, changes in humidity, temperature, or mechanical load on the gantry could certainly change the center-to-center distance enough to cause problems. Traditionally, router builders would open one hole on either side to "float" one of the two shafts and/or install larger steppers to overcome the additional friction caused by "moving the wood". A simple fix to holding accurate center-to-center distances on a wood-based router is an alignment plate for each side. It would be 1/4" to 3/8" thick, could sit in a nifty pocket milled into the gantry side, and be held in with a few wood screws.
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Now the bad news about this solution. I am a supervisor in a shop with CNC vertical machining centers. The AQuick z-axis block is a good piece of machining that I would not do myself given the attractive price. Having said that,
any small deviations in alignment or concentricity from the left and right bearings on either shaft will cause the center-to-center distances to be ever-so-slightly different. My alignment plates caused a slight binding on one side when the z-axis got to within 2" of the left gantry alignment bracket. Thinking it was my machining accuracy, I swapped the left and right alignment plates. The problem remained on the left side. It is only a few 0.0001".
The ultimate solution would be a set of alignment plates where each plate consisted of overlapping joints. The top half would be permanently attached. The bottom half would be locked into place against the top half using the z-axis itself as an alignment fixture. No measuring, no fuss.
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The AQuick rod holder thingies I see in the pictures of the plastic version would allow adjustment for small deviations from side to side. The benefit of the above alignment plate halves being locked together should keep the center-to-center distance the same even if the wood does not cooperate.
Note - I am aware the bracket drawn does not allow for lead screw clearance. I did something different for the lead screw mounting. Slight modifications would allow for conventional mounting of the screw.