Great progress, hope you will let us follow you to completion. Having read a lot of build logs here, it is so disappointing when a promising build tails off so you never learn if the design and approach had any merit! There are 5 builders with finished machines in the Gallery Post from 15 pagesx20 DIY build logs, so that is less than 2% that actually complete their machine and stick around long enough to share. It gives me pause, but you are giving me hope!

Not to criticise, but to show I am listening to the grey beards here, and want to copy much you have done:
I understand the frequent suggestion of having the gantry (X) separate and adjustable from the Y linear bearings for squaring up etc. You clearly still have access to your Y linear bearing screws, so adjustment is still available. However would turning the thick Y linear bearing plate into two, with the lower fixed to the bearings and the upper fixed to the gantry and then bolt and pin them when XY aligned make things more modular and adjustable?