How did you align it ? The X/Y axis often do not perfectly match the X/Y “lines” on the wasteboard
When I need something align with X or Y axis of the machine, I tend to use a vbit to engrave a shallow line on the wasteboard along the desired axis, and then use that visual cue to align my stock.
But more often than not I try to avoid having to align anything precisely: start from a piece of stock that is slightly larger than required, and have the machine do the profile cut to the final outer dimensions. That way even if the stock was not perfectly aligned initially, the final piece and all its inner features are still perfectly aligned/positioned.
I made my reference edge out of a strip of plywood, and made a cut after mounted down to get reference edge aligned with machine travel direction. I had made a relief cut on the bottom side of the plywood before mounting.
I made a small square jig on my shapeoko 4, for when I want to do precise holes/pockets like what you’re doing. I use 1/4" dowel pins to mount the jig on when I need it.
It also works great for machining operations that require changing the orientation of the workpiece, since it can ensure it’s in the same spot every single time. With the jig, I’m getting just +/- 0.025mm of deviation across the entire length of the jig which is way good enough for most projects.
If you use the CNC to mill out holes into the wasteboard, it will be parallel with the router’s relative path. I machined this out of delrin, for use with aluminum work pieces. But if you plan on doing wood, you could machine it out of aluminum (just so you can find the precise home position with a multimeter and a probe)