Solved Z layers not stacking nicely, vibrations in the print along X and Y

The stock values are (IMHO) silly:

#define DEFAULT_MAX_ACCELERATION {9000,9000,100,10000} // X, Y, Z, E maximum start speed for accelerated moves. E default values are good for Skeinforge 40+, for older versions raise them a lot.

#define DEFAULT_ACCELERATION 1300 // X, Y, Z and E max acceleration in mm/s^2 for printing moves /robo
#define DEFAULT_RETRACT_ACCELERATION 3000 // X, Y, Z and E max acceleration in mm/s^2 for retracts

// The speed change that does not require acceleration (i.e. the software might assume it can be done instantaneously)
#define DEFAULT_XYJERK 17.0 // (mm/sec)
#define DEFAULT_ZJERK 0.4 // (mm/sec)
#define DEFAULT_EJERK 5.0 // (mm/sec)

I have my acceleration numbers significantly less.
DEFAULT_MAX_ACCELERATION in particular is about 1/3 of that.

Others you may want to experiment with.

 

I assume you did not look at the examples I linked to.
Here they are again, pretty well spelled out with what-is-what:

M201 X1000 Y1000 Z100 E2000 ;set max printing acceleration X/Y/Z/Extruder
M205 X15 Z0.4 E5 ; set max x&y, z, e jerk (speed change does not require acceleration)

 

Starting GCode script is the logical place for it if you are not adjusting the firmware.

Also, I would not worry about the extruder settings.

 

Yep

More inline with what the hardware can actually do.