If you are trying to put the screw close over the linear blocks, why don't you sink the nut in to the plate and drop the screw down? How are you going to keep the cuttings out of the screws? You have made it from heavy section to cut aluminium but that will not help you get the speed to cut wood efficiently. If your gantry weighs 50 lbs then you need 50 lbf plus the cutting force to accelerate it at one G.

OTOH I think you need to build something wrong and then fix it with the Mk2. Understanding CNC design does rather come with experience. Getting it wrong is not actually a bad idea.