Hi Carlokko.
Please see my recent posts on this subject which are summarised below.
http://www.stepcraft-systems.com/en/forum/assembly-and-maintenance/3777-stepcraft-is-an-unbaked-product-and-i-hate-it#39996
http://www.stepcraft-systems.com/en/forum/operation/3176-clicking-noise-x-y-axes#40100
I believe that the majority of Y axis 'mechanical tuning' issues that people are experiencing, particularly with the larger footprint machines are due to two factors (assuming that your track roller assemblies are correctly set and run freely in the extrusions without excessive play):
(a) Screw mounting hole size and/or position constraining the end plates from aligning correctly.
(b) the lack of some free play in the bearing holes in the end plates.
The instruction manual does not stipulate how to address these issues because they involve modifying the machine.
1. It seems counter-intuitive but I understand that there needs to be some free play in the lead screw mechanism, especially at the non driven end of the axis. Largely speaking, the track roller and extrusion assembly provide the alignment while the lead screw & lead nut assembly provide the linear drive. The two functions are not fully interdependent. This must be a characteristic of the lead nut/lead screw linear drive type and will be more of an issue the larger the machine.
Note that the aluminum T slot bed is machined to a precise tolerance and will therefore constrain the available extrusion movement.
You will almost certainly need to remove the orange powder coating from the bearing seats. You might also need to remove the powder coating and file away some of the metal in the end plate screw mounting holes to provide sufficient screw clearance to avoid them misaligning the extrusions or applying stress to the lead screws when the mounting screws are tightened. When the end plates are tightened up to the extrusions, both lead screws should turn easily by hand/fingertips.
Take care not to drive the Y axis too quickly by hand operation of the drive belt or the generation of back EMF will risk burning out the Y axis chip in the control PCB. A sensible precaution is to disconnect the four wires from the control PCB.
2. Once there is sufficient free play in the lead screw(s) and the mounting screw holes are big enough to stop the end plate misaligning the extrusions when the screws are tightened, align them by loosening the end plate or gantry, drive the track rollers/gantry to one end, align each (in the case of Y axis) then tighten up the end plate screws. This process acts to self-align the assembly.
3. Resistance in the stepper motor (when it is de-energised of holding torque, obviously) might be due to the superglue used to fix the bearing in place bleeding onto the shaft and causing fouling. Exercising it by hand might free it off. If not, remove and clean.
4. As an additional precautionary measure if things are still not going well is to reduce the full travel speed (G00) from 3,000 to maybe 2,250 to 2,500 mm/min in UCCNC or Mach 3 or whichever control software you are using.
I hope the above insights help you resolve your issues.
Regards.
Doug