Have you thought of using a link rod between the two motors, as most GRBL and the MKSDLC32 MAX boards although supplying two y-axis driver outputs, it is rare to find two separate Y Limit swithes for each motor, obviously when the motors are powered down there is a case where the alignment between them can be lost, so each end of the axis can become skewed, but connecting the shafts end to end with a link rod as done in many smaller machines using one motor to drive both sides of the Y axis, it would keep them in sync when the motors are not powered, then only one limit switch would be needed after the initial setup of squaring the Y axis.
As to wobble I had the same issue in both directions that drove me mad, but found my acceleration setting was to high so on each end ofthe Y Movement between lines there was an initial wobble wave over the first inch as the dpi disance movement does not allow time for the initial acceleration jolt to settle the weight/inertia of the X carriage over such a small movement. But such a long wobble you must have some flex in the carriage mounting the laser head as previously mentioned.
