Z axis cuts in the air - SOLUTION

Hi - everyone. Just to mention after much head scratching and with help from people and just tweaking settings here and there - I have finally got things working.
How did I do it? not quite sure I know fully.
One thing that really helped was having a look at someone else's INI file and comparing it with mine.
Anyway, this is my INI file and HAL now for anyone who's interested.
Thanks to all who tried their best to help.
Regards



# Generated by stepconf 1.1 at Sun Sep 6 13:24:54 2020
# If you make changes to this file, they will be
# overwritten when you run stepconf again

[EMC]
MACHINE = my-mill2
DEBUG = 0

[DISPLAY]
DISPLAY = axis
EDITOR = gedit
POSITION_OFFSET = RELATIVE
POSITION_FEEDBACK = ACTUAL
ARCDIVISION = 64
GRIDS = 10mm 20mm 50mm 100mm 1in 2in 5in 10in
MAX_FEED_OVERRIDE = 1.2
MIN_SPINDLE_OVERRIDE = 0.5
MAX_SPINDLE_OVERRIDE = 1.2
DEFAULT_LINEAR_VELOCITY = 5.00
MIN_LINEAR_VELOCITY = 0
MAX_LINEAR_VELOCITY = 20.00
INTRO_GRAPHIC = linuxcnc.gif
INTRO_TIME = 5
PROGRAM_PREFIX = /home/jeff65/linuxcnc/nc_files
INCREMENTS = 5mm 1mm .5mm .1mm .05mm .01mm .005mm

[FILTER]
PROGRAM_EXTENSION = .png,.gif,.jpg Greyscale Depth Image
PROGRAM_EXTENSION = .py Python Script
png = image-to-gcode
gif = image-to-gcode
jpg = image-to-gcode
py = python

[TASK]
TASK = milltask
CYCLE_TIME = 0.010

[RS274NGC]
PARAMETER_FILE = linuxcnc.var

[EMCMOT]
EMCMOT = motmod
COMM_TIMEOUT = 1.0
COMM_WAIT = 0.010
BASE_PERIOD = 37851
SERVO_PERIOD = 1000000

[HAL]
HALFILE = my-mill2.hal
HALFILE = custom.hal
POSTGUI_HALFILE = custom_postgui.hal

[TRAJ]
AXES = 3
COORDINATES = X Y Z
LINEAR_UNITS = mm
ANGULAR_UNITS = degree
CYCLE_TIME = 0.010
DEFAULT_VELOCITY = 2.00
MAX_VELOCITY = 20.00

[EMCIO]
EMCIO = io
CYCLE_TIME = 0.100
TOOL_TABLE = tool.tbl

[AXIS_0]
TYPE = LINEAR
HOME = 0
MAX_VELOCITY = 12.5492060976
MAX_ACCELERATION = 13.0
STEPGEN_MAXACCEL = 16.25
SCALE = -2000.0
FERROR = 1
MIN_FERROR = .25
MIN_LIMIT = 0
MAX_LIMIT = 168.0
HOME_OFFSET = 160
HOME_SEARCH_VEL = -3.000000
HOME_LATCH_VEL = 0.20000
HOME_FINAL_VEL = 5
HOME_IGNORE_LIMITS = YES
HOME_SEQUENCE = 1

[AXIS_1]
TYPE = LINEAR
HOME = 0
MAX_VELOCITY = 12.5492060976
MAX_ACCELERATION = 13.0
STEPGEN_MAXACCEL = 16.25
SCALE = -2000.0
FERROR = 1
MIN_FERROR = .25
MIN_LIMIT = 0
MAX_LIMIT = 79
HOME_OFFSET = 70
HOME_SEARCH_VEL = -3.000000
HOME_LATCH_VEL = 0.20000
HOME_FINAL_VEL = 5
HOME_IGNORE_LIMITS = YES
HOME_SEQUENCE = 2

[AXIS_2]
TYPE = LINEAR
HOME = 0
MAX_VELOCITY = 12.5492060976
MAX_ACCELERATION = 13.0
STEPGEN_MAXACCEL = 16.25
SCALE = -2000.0
FERROR = 1
MIN_FERROR = .25
MIN_LIMIT = -65
MAX_LIMIT = 0
HOME_OFFSET = -5
HOME_SEARCH_VEL = -1.000000
HOME_LATCH_VEL = 0.250000
HOME_FINAL_VEL = 1
HOME_IGNORE_LIMITS = YES
HOME_SEQUENCE = 0


HAL
# Generated by stepconf 1.1 at Sun Sep 6 13:24:54 2020
# If you make changes to this file, they will be
# overwritten when you run stepconf again
loadrt trivkins
loadrt [EMCMOT]EMCMOT base_period_nsec=[EMCMOT]BASE_PERIOD servo_period_nsec=[EMCMOT]SERVO_PERIOD num_joints=[TRAJ]AXES
loadrt hal_parport cfg="0 out"
setp parport.0.reset-time 1500
loadrt stepgen step_type=0,0,0
loadrt charge_pump
net estop-out charge-pump.enable iocontrol.0.user-enable-out
net charge-pump <= charge-pump.out

addf parport.0.read base-thread
addf stepgen.make-pulses base-thread
addf charge-pump base-thread
addf parport.0.write base-thread
addf parport.0.reset base-thread

addf stepgen.capture-position servo-thread
addf motion-command-handler servo-thread
addf motion-controller servo-thread
addf stepgen.update-freq servo-thread
net spindle-cmd-rpm <= motion.spindle-speed-out
net spindle-cmd-rpm-abs <= motion.spindle-speed-out-abs
net spindle-cmd-rps <= motion.spindle-speed-out-rps
net spindle-cmd-rps-abs <= motion.spindle-speed-out-rps-abs
net spindle-at-speed => motion.spindle-at-speed
net spindle-cw <= motion.spindle-forward

net estop-out => parport.0.pin-01-out
net xstep => parport.0.pin-02-out
setp parport.0.pin-02-out-reset 1
net xdir => parport.0.pin-03-out
net ystep => parport.0.pin-04-out
setp parport.0.pin-04-out-reset 1
net ydir => parport.0.pin-05-out
net zstep => parport.0.pin-06-out
setp parport.0.pin-06-out-reset 1
net zdir => parport.0.pin-07-out
net astep => parport.0.pin-08-out
setp parport.0.pin-08-out-reset 1
net adir => parport.0.pin-09-out
net spindle-cw => parport.0.pin-14-out
net charge-pump => parport.0.pin-16-out
net xenable => parport.0.pin-17-out
net home-x <= parport.0.pin-10-in
net home-y <= parport.0.pin-11-in
net home-z <= parport.0.pin-12-in

setp stepgen.0.position-scale [AXIS_0]SCALE
setp stepgen.0.steplen 1
setp stepgen.0.stepspace 0
setp stepgen.0.dirhold 29551
setp stepgen.0.dirsetup 29551
setp stepgen.0.maxaccel [AXIS_0]STEPGEN_MAXACCEL
net xpos-cmd axis.0.motor-pos-cmd => stepgen.0.position-cmd
net xpos-fb stepgen.0.position-fb => axis.0.motor-pos-fb
net xstep <= stepgen.0.step
net xdir <= stepgen.0.dir
net xenable axis.0.amp-enable-out => stepgen.0.enable
net home-x => axis.0.home-sw-in

setp stepgen.1.position-scale [AXIS_1]SCALE
setp stepgen.1.steplen 1
setp stepgen.1.stepspace 0
setp stepgen.1.dirhold 29551
setp stepgen.1.dirsetup 29551
setp stepgen.1.maxaccel [AXIS_1]STEPGEN_MAXACCEL
net ypos-cmd axis.1.motor-pos-cmd => stepgen.1.position-cmd
net ypos-fb stepgen.1.position-fb => axis.1.motor-pos-fb
net ystep <= stepgen.1.step
net ydir <= stepgen.1.dir
net yenable axis.1.amp-enable-out => stepgen.1.enable
net home-y => axis.1.home-sw-in

setp stepgen.2.position-scale [AXIS_2]SCALE
setp stepgen.2.steplen 1
setp stepgen.2.stepspace 0
setp stepgen.2.dirhold 29551
setp stepgen.2.dirsetup 29551
setp stepgen.2.maxaccel [AXIS_2]STEPGEN_MAXACCEL
net zpos-cmd axis.2.motor-pos-cmd => stepgen.2.position-cmd
net zpos-fb stepgen.2.position-fb => axis.2.motor-pos-fb
net zstep <= stepgen.2.step
net zdir <= stepgen.2.dir
net zenable axis.2.amp-enable-out => stepgen.2.enable
net home-z => axis.2.home-sw-in

net estop-out <= iocontrol.0.user-enable-out
net estop-out => iocontrol.0.emc-enable-in

loadusr -W hal_manualtoolchange
net tool-change iocontrol.0.tool-change => hal_manualtoolchange.change
net tool-changed iocontrol.0.tool-changed <= hal_manualtoolchange.changed
net tool-number iocontrol.0.tool-prep-number => hal_manualtoolchange.number
net tool-prepare-loopback iocontrol.0.tool-prepare => iocontrol.0.tool-prepared