You aren't using the probe to set the Z0 position at all. Your homeall is still using the Z endstop.

This isn't a problem in itself, but you must set the Z0 position with the probe eventually.

I suggest you modify beg.g like this

G90 G1 X100 Y100 Z5 F6000 ; move the probe to center of bed G30 ; probe center of bed G30 P0 X30 Y115 Z-99999 ; probe near a leadscrew, half way along Y axis G30 P1 X220 Y115 Z-99999 S2 ; probe near a leadscrew and calibrate 2 motors G1 X100 Y100 Z5 F6000 ; move the probe to center of bed G30 ; probe center of bed

You'll need to recreate your mesh after doing that as well.