The gantry corner bracket could use a notch. Now I’m just guessing how high the bracket needs to extend beyond the extrusion. At least enough for the motors but ideally they’d sit flush with the extrusion end. It would also help with aligning the brackets equally on both gantry sides.
Yep, we’re already planning to add notches to the Gantry Corner Brackets and Toolbays in v1.3 
Thanks for the feedback though!
I just maxed the height with the t-nut on both sides