If I understand your dwg correctly I would put the hiwin rail on the TOP of the section. This gives natural vertical spacing of the gantry, provides a nice way to connect it to the bearings, and gives you the option of epoxy leveling the surface to get the bearings level with each other (LH and RH side).

Do you know how much vertical clearance and travel you want between the spindle and bed? It looks very close at the moment so you may need to make the side sections deeper to raise the gantry. Don't commit to the side bits until you have drawn the Y, Z and spindle and got the top/bottom travel worked out as this will dictate the X rail height to a degree.