Hey Raul, when checking the spindle/router bearings for lateral movement, recommend also checking for vertical movement by pushing the bit up and down. This checks the Z-carriage guides and ball-nut for slop as well as the spindle/router armature. The Dewalt router that came with my Shapeoko 3 had about .5mm play vertically. Turned out that the molded plastic top bearing seat was oversize. This messed with my depth of cut/max depth accuracy until I figured it out.
That being said, I noticed that the deep grooves are somewhat evenly spaced in the Y direction. Looking to the experts to confirm, but wondering if the problem could be flat spot(s)/crack(s) in the Y-axis v-wheels? Maybe one or more eccentric nuts are too tight causing a weak spot in the v-wheel to deform every rotation? I would visually inspect all 4 v-wheels, and rails, on each side. You might even just swap the uppers for the lowers and see if it makes a difference.
Hope that helps.
Brian