In my X and Y off by 1% original post, I tried measuring the offset as the machine jogged away from center, but jogging is a little different than cutting. Since your pegboard has a grid based layout, can you maybe measure the offset of each cut as it moves from the origin point and map out how it deviates from the design? (millimeters please!)
What I found, is the problem gets worse at the edges, which is on par with @dlang 's cool mapping tool. By moving my corner mounts out on the X axis, clipping the ears, and running a super large calibration, I was able to get the machine down to a 2mm deviation about 1" from the edge of the work piece.
BTW, looks like a super cool design! Would love to see more pics.