@Torchit1 Wow, that's an impressive test file.
It is difficult for me to tell what is causing this issue, it could be electrical noise resulting in an overstep or it could be Y-axis backlash "catching up" and causing it.
You mentioned disabling bi-directional mode, so it sounds like you have a backlash issue on the X-axis. I can run at 3000 with no issues so your machine may need some mechanical adjustments, perhaps the wheels are binding?
Steppers with encoders would probably not help, or what I suspect you are talking about are the servo motors which have step and direction drivers so act like steppers. The problem with servos is they tend to hunt without good control logic, but are generally the better technology.
Have you tried setting the Y-max speed to 1000 so you can use 2000 or more for the X-axis and the Y will remain lower? That may be a reasonable band-aid. To do that enable debug mode and type $111=1000 then press enter.