The X axis bearing connection looks better now. For info you can buy ballnut mounts off e-bay which are longer than the one you have drawn so give a bigger footprint and are stiffer. They are connected by 4 bolts, not 2 which is better.
http://www.ebay.co.uk/itm/Ball-Nut-M...QAAOSwHnFVjdoi


On the Y axis the 2 ways of mounting the ballscrews you have drawn are probably similar in stiffness so go for what seems most practical to make - but how will you mount that box section end-on? You mention turning it around which would be better.