I came up with the idea of placing a ruler across both the supporting rails and the lead-screw of the x-axis as close to one of the support as possible with the tip of the ruler resting on the gantry base. Scoring a line against the ruler tip I could then take a measurement with the calipers of how far the line was away from the side of the gantry base. I used the calipers to transfer this line to the opposite support. I used the same technique to adjusting the gantry near the other support lining up the ruler with the score line. The x-axis was now true to the gantry.