I'm going to try and work on some drawings this weekend but pretty sure i have a plan. For gantry plates I am thinking of 0.500" 6061, vertical of course, that will bolt with socket cap bolts to a piece of 0.750" 6061 that will ride on the bearing blocks. I would mill a press fit groove in the 0.750" plate that the gantry plates would index in and the bolts would be inserted from underneath. I can then machine a groove in the bottom face of the 0.750" plate and bolt a piece of 0.500" to it that has a bore and screw holes for the ballscrew into it. For the y axis, axis across the gantry, i would have a piece of 0.500" plate across the back of the gantry the the ballscrew supports would bolt to and use 2 pieces of the same material on the face of the gantry by the spindle which would leave a small gap for a dust shield.
For the grooves in the 0.750" plate, do you think that a depth of 0.250" would be sufficient so long as the edge of the surface being bolted to it was milled so that it was perpendicular to the uprights? I know this design will leave me with a fairly heavy gantry but that should also inhibit resonance.