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Speeds in Printrun are in mm/min. I presume you have already set DEFAULT_MAX_FEEDRATE {30, 30, 0.35, 4.17} in firmware, right? That will allow you to reach speeds around 30mm/s*60 s = 1800mm/min in X and Y axis. Anything above this is reduced by firmware for safety reasons no matter what you set in Printrun. If you want to test higher speeds you have to change DEFAULT_MAX_FEEDRATE to something like {50, 50, 1, 5}. That will let you do up to 3000mm/min in X and Y, 60mm/min in Z and 300mm/min with extruder, but ...

Concerning Cura. Well if maximal feedrate for extruder is set to 4.17mm/s in firmware, it will hardly do 10mm/s retraction in any slicing program. Even if 4.17mm/s is too much, and your machine can do only let say 3.5mm/s, you are asking for trouble.

Pumping Amps to motor will help only if the motor can run that quick. If not, it will just heat more and eventually burn while chopping. Vref depends on the driver you are using and sense resistor, that is near the trimmer. Check this web page for correct settings: http://reprap.org/wiki/Pololu_stepper_driver_board I think you can safely use 0.09A to 0.15A per one motor (0.18-0.3A in Z axis). That is 0.07-0.12V with common A4988 or 0.045V-0.075V with DRV8522 (you will have to dig up the datasheet for this one).

Actually retraction is not causing the layer shift. It is the movement speed of X and Y axis or movement acceleration. Remember that these motors in ToyREP can do safely only 12.5mm/s (doesn't matter if it is print speed or movement speed) and everything above this value is a bonus. Try to set speeds in slicer to this and than go up in small steps (like 2.5mm/s) while printing the cube or what ever test model. Than set your final numbers in firmware, so you will not accidentally try to push the machine above the limit with some wrong settings in slicer. If that will not help problem is probably in too high acceleration and/or jerk.