Looks much better to me.

Putting the Y-axis ballscrew along the top is not a good place since it's so far from the cutting force. The Y-axis bearings obviously don't provide any support parallel to the Y-axis, so they would be pushed slightly in that direction. If the screw is lower down it's less of a problem. The best place would be to put it on the opposite side, but that's a bit in the way...

Not sure about the way you've mounted the X-axis linear bearings. Though the forces might by more even, it's much much harder to get them parallel. I'd keep the orientation you had previously. I think it's best to have them that way anyway as the forces are not even - you've got the weight of the gantry loading them in one direction.