Changed the homing position in printer settings to 180 and the Y axis is working correctly.
Move increments are always the same now
Steps per mm are the same as are the length, done the M502 M500 commands.
I think I should change the position of the X endstop, moving it to the side where the Y endstops are would be better for machine control, right now when I run the dry test g code (which is made n repetier, only without the start procedure, and G92 X0 Y0 Z0 ) Y works the way it should but X is moving in the direction where the endstop is and it should be moving the opposite direction. The Z was moving the wrong direction, I've inverted the direction in the firmware and now it is working properly.
Besides that there is one more problem I've encountered- extruder stepper is not working.
Tried swapping the A4988 driver with the one from the Felix 3d printer that is working and also nothing happened.
Turned on the hot end, also nothing (I thought maybe it was due to cold extrusion safety feature) what would be the test g code command to try