I need to know how and what to adjust the left and/or right hand side of the X gantry to ensure the z axis is the same on both sides of the machine. I made some 3D printed dial indicator holders and the left side reads 10.94mm and the right side reads 9.40mm from the gantry to the spoil board. (The spoil board is the stock one. ) My machine is in an enclosure so no matter what I need to do, its not going to be fun.
Skim cut a 2nd waste board on top of the original one, this ensure Z is parallell with your work surface 
Make sure your waste board is secure were it attaches to the rails, when you built the sub frame under the waste board did you make sure as you connected the rails to ech other and tighten them down at each of the contact points that they met up perfect? there is some play in the brackets. Also make sure you don’t have any “Play” were the “Y” rails attach to the risers. If all else fails you can loosen your spoil board and simply shim it on the low side using some paper or chipboard if you don’t want to skim cut your waste board.
i just leveled it using a 1/4" bit