It's just occurred to me that your gantry has very poor torsional stiffness. Normally that's not a problem as with two ballscrews it can't twist, however with only one nut in the middle when the cutter is near either edge of the bed the gantry can twist causing deflection. Given the tolerances you require that could cause problems. You're essentially only relying on the joint between the gantry back plate as sides, so I'd be inclined to reinforce that. The rail mount blocks will help...also don't remember what joining the bottom of the gantry sides, that will make a difference.