Z axis homing and travel

Hello, I have been re-fitting my Prolight-1000 mill to be CNC controlled again (previous owner removed all CNC components and rigged it to be manual controls). I have gotten X and Y axis to properly home and all that but the Z axis just doesn't seem to make sense to me. From what I have read I want my home switch to be at the top of my travel and have that be considered (in my case of 9 inch Z travel) -9.0 minimum travel to 0.0 for max travel (being spindle touching the table). I was kind of confused on whether the top of my travel would be 0.0 or -9.0 and also how to get it to show right in the axis interface. I inverted Z direction so that goes down towards the table (and thus towards 0 from the negative direction) but it shows the opposite direction in the interface. Any help is much appriciated.
Hal file:  
INI file: 

I have my Z home at top but linuxcnc sees that as a positive number. My travel min is -0.003 (all the way down) and max is 7.65 with home switch at 7.6 and home at 7.5. I am pasting my Z section from the ini file which has my specific home settings. Check your home settings in the hal file as you have a line for min-home-U, not Z. Mine are all the same which would be max-home-z. Also you will need to define the Z settings the same way that your Y and X are done.

My settings are carried over from earlier versions of lcnc so the syntax may be a bit different.

#*** AXIS_Z *******************************
[AXIS_Z]
MAX_VELOCITY = 5.700069312842844
MAX_ACCELERATION = 20.0
MIN_LIMIT = -0.003
MAX_LIMIT = 7.65

[JOINT_3]
TYPE = LINEAR
HOME = 7.5
MIN_LIMIT = -0.003
MAX_LIMIT = 7.65
MAX_VELOCITY = 5.700069312842844
MAX_ACCELERATION = 20.0
STEPGEN_MAXACCEL = 25.0
SCALE = 4064.0
FERROR = 0.05
MIN_FERROR = 0.01
HOME_OFFSET = 7.6000
HOME_IGNORE_LIMITS = YES
HOME_SEARCH_VEL = 0.1450
HOME_LATCH_VEL = 0.1450
HOME_FINAL_VEL = 0.1450
HOME_SEQUENCE = 0
#******************************************

For mills, Z should be at the top and near or 0 on DRO, -9 in your case when touching table or at the lowest point of travel.
Although almost every way can be made to work with LinuxCNC, that is the standard way and saves a lot of trouble with post processors in CAM as those will always have 0 at the top of the material and go negative when plunging in.

Okay, I was getting confused trying to figure out what the standard is. Thank you,

I\m also having some problems with my Z homing. My z axis home switch is at the top of my Z axis so it is as far to the plus end of my travel that it can go. If the home is z-0 then I have 8" of travel in the minus direction before I would hit an end stop. I've tried various changes in the ini file but nothing seems to work. The settings are as follows:

[AXIS_Z]
MAX_VELOCITY = 1.0
MAX_ACCELERATION = 30.0
MIN_LIMIT = .0001
MAX_LIMIT = -7

[JOINT_3]
TYPE = LINEAR
HOME = 0.0
FERROR = 0.5
MIN_FERROR = 0.05
MAX_VELOCITY = 1.0
MAX_ACCELERATION = 30.0
# The values below should be 25% larger than MAX_VELOCITY and MAX_ACCELERATION
# If using BACKLASH compensation STEPGEN_MAXACCEL should be 100% larger.
STEPGEN_MAXVEL = 1.25
STEPGEN_MAXACCEL = 37.50
P = 786.115316828056
I = 0.0
D = 0.0
FF0 = 0.0
FF1 = 1.0
FF2 = 0.0
BIAS = 0.0
DEADBAND = 0.0
MAX_OUTPUT = 0.0
# these are in nanoseconds
DIRSETUP = 20000
DIRHOLD = 20000
STEPLEN = 20000
STEPSPACE = 20000
STEP_SCALE = 8127.9997
MIN_LIMIT = -7.0
MAX_LIMIT = 0.001
HOME_OFFSET = 0.000000
HOME_SEARCH_VEL = 0.050000
HOME_LATCH_VEL = 0.016667
HOME_FINAL_VEL = 0.016667
HOME_USE_INDEX = NO
HOME_SEQUENCE = 1

Any idea where I'm going wrong here?