It looks like you have the opportunity to bolt through from the horizontal carriage plate to the bottom of the gantry extrusion - this will greatly rigidise the axial movement of the gantry and reduce the requirement for the side plates over a design where the gantry extrusion is well up in the air and the side plates are taking all the strain. Regarding position of the rails on the gantry, top and bottom spaces them further apart than on the front giving the opportunity for greater rigidity and keeps the Z axis assembly close to the gantry, but it will lose you clearance in the Z axis. Top and front (bottom) is an in-between solution that some people use.