Sorry to bring bad news, but you've put the joints on the plates the wrong way round. Normally people do it such that the top and bottom plates, to which the Y-axis bearings are mounted can move up/down a little then be bolted down to accommodate variation in the Y-axis rail spacing. You had it right in the drawing in post #87.
There shouldn't be any need to start changing things as long as the top and bottom sides of the plates are square to make the bearing plates parallel. If so then you just need to make the gantry such that there's a little bit of adjustment in at least one of the Y-axis rails. The other solution is leave the bigger plate on the Z-axis as it is and cut the smaller one to fit between and make that joint adjustable.