Hal file:
# pinout config file for 3 channel Xylotex drive
# using a parport for I/O
#
# first load the parport driver
loadrt probe_parport
loadrt hal_parport cfg="0x0378"
#
# next connect the parport functions to threads
# read inputs first
addf parport.0.read base-thread 1
# write outputs last
addf parport.0.write base-thread -1
#
# finally connect physical pins to the signals
linksp Xstep parport.0.pin-02-out
linksp Xdir  parport.0.pin-03-out
linksp Ystep parport.0.pin-04-out
linksp Ydir  parport.0.pin-05-out
linksp Zstep parport.0.pin-06-out
linksp Zdir  parport.0.pin-07-out

# create a signal for the estop loopback
linkpp iocontrol.0.user-enable-out iocontrol.0.emc-enable-in

# create signals for tool loading loopback
linkpp iocontrol.0.tool-prepare iocontrol.0.tool-prepared
linkpp iocontrol.0.tool-change iocontrol.0.tool-changed

# Limit Switches
#newsig Z-pos-limit bit
#linkps parport.0.pin-10-in => Z-pos-limit
#linksp Z-pos-limit => axis.2.pos-lim-sw-in

newsig homeswitches bit
linkps parport.0.pin-10-in => homeswitches
linksp homeswitches => axis.0.home-sw-in
linksp homeswitches => axis.1.home-sw-in
linksp homeswitches => axis.2.home-sw-in
# Shared home/limit switches
# If I uncomment more than one link below then
# nothing will home. It only sees the switches as limits???
# It works as I expected when only one link is put here.
#linksp homeswitches => axis.0.pos-lim-sw-in
#linksp homeswitches => axis.1.pos-lim-sw-in
linksp homeswitches => axis.2.pos-lim-sw-in

My ini file:
# EMC controller parameters for generic controller. Make these what you need
# for your system.

# General note: Comments can either be preceded with a # or ; - either is
# acceptable, although # is in keeping with most linux config files.

# Settings with a + at the front of the comment are likely needed to get 
# changed by the user.
# Settings with a - at the front are highly unneeded to be changed
###############################################################################
# General section 
###############################################################################
[EMC]

#- Version of this INI file
VERSION =               $Revision: 1.8.2.3 $

#+ Name of machine, for use with display, etc.
MACHINE =               EMC-HAL-STEP-IN

#- Name of NML file to use, default is emc.nml
NML_FILE =              emc.nml

#+ Debug level, 0 means no messages. See src/emc/nml_int/emcglb.h for others
DEBUG = 0
# DEBUG =               0x00000007
# DEBUG =               0x7FFFFFFF

###############################################################################
# Sections for display options 
###############################################################################
[DISPLAY]

#+ Name of display program, e.g., xemc
#DISPLAY =              axis
# DISPLAY =              usrmot
DISPLAY =              mini
# DISPLAY = 		tkemc
# Cycle time, in seconds, that display will sleep between polls
CYCLE_TIME =            0.200

#- Path/name of help file
HELP_FILE =             tkemc.txt

#- Initial display setting for position, RELATIVE or MACHINE
POSITION_OFFSET =       RELATIVE

#- Initial display setting for position, COMMANDED or ACTUAL
POSITION_FEEDBACK =     ACTUAL

#+ Highest value that will be allowed for feed override, 1.0 = 100%
MAX_FEED_OVERRIDE =     1.2

#- Prefix to be used
PROGRAM_PREFIX = /home/mic/emc2/nc_files

#- Introductory graphic
INTRO_GRAPHIC =         emc2.gif
INTRO_TIME =            2


###############################################################################
# Task controller section 
###############################################################################
[TASK]

#- Name of task controller program, e.g., bridgeporttask
TASK =                  milltask

#- Cycle time, in seconds, that task controller will sleep between polls
CYCLE_TIME =            0.010

###############################################################################
# Part program interpreter section 
###############################################################################
[RS274NGC]

#- File containing interpreter variables
PARAMETER_FILE =        stepper.var

###############################################################################
# Motion control section 
###############################################################################
[EMCMOT]

#- Name of the motion controller to use (only one exists for nontrivkins)
EMCMOT =                motmod

#- Key for real OS shared memory, e.g., for simulated motion
SHMEM_KEY =             111

#- Timeout for comm to emcmot, in seconds
COMM_TIMEOUT =          1.0

#- Interval between tries to emcmot, in seconds
COMM_WAIT =             0.010

#+ Base task period, in nanosecs - this is the fastest thread in the machine
#BASE_PERIOD =           50000
#BASE_PERIOD =           14000
BASE_PERIOD =		 22000
#- Servo task period, in nanosecs - will be rounded to an int multiple of BASE_PERIOD
SERVO_PERIOD =          1000000
#- Trajectory Planner task period, in nanosecs - will be rounded to an
#   integer multiple of SERVO_PERIOD
TRAJ_PERIOD =           10000000

###############################################################################
# Hardware Abstraction Layer section
###############################################################################
[HAL]

# The run script first uses halcmd to execute any HALFILE
# files, and then to execute any individual HALCMD commands.
#

# list of hal config files to run through halcmd
#+ files are executed in the order in which they appear
HALFILE =               core_stepper.hal
HALFILE =               xylotex_pinout.hal
#HALFILE =               standard_pinout.hal

#- list of halcmd commands to execute
# commands are executed in the order in which they appear
#HALCMD =                save neta

###############################################################################
# Trajectory planner section
###############################################################################
[TRAJ]
#+ machine specific settings
AXES =                  3
# COORDINATES =         X Y Z A B C
COORDINATES =           X Y Z
HOME =                  0 0 0
LINEAR_UNITS =          inch
ANGULAR_UNITS =         degree
CYCLE_TIME =            0.010
DEFAULT_VELOCITY =      0.0167
MAX_VELOCITY =          0.275
DEFAULT_ACCELERATION =  1.5
MAX_ACCELERATION =      1.650

###############################################################################
# Axes sections
###############################################################################

#+ First axis
[AXIS_0]



# NOTE:  the step generator module applies its own limits to
# acceleration and velocity.  We have discovered that it needs
# to have a little "headroom" over the accel by the trajectory
# planner, otherwise it can fall slightly behind during accel
# and later overshoot as it catches up.  In the long term we
# hope to come up with a clean fix for this problem.  In the
# meantime, please set STEPGEN_MAXACCEL below to a few percent
# higher than the regular acceleration limit MAX_ACCELERATION
TYPE =                          LINEAR
HOME =                          -1.000
MAX_VELOCITY =		0.275
MAX_ACCELERATION =              1.5
STEPGEN_MAXVEL =        0.3025
STEPGEN_MAXACCEL =              1.65
BACKLASH =                      0.000
INPUT_SCALE =                   28800
OUTPUT_SCALE =                  1.000
 MIN_LIMIT =                     -36.0
 MAX_LIMIT =                     .10
FERROR =                        0.050
MIN_FERROR =                    0.010
HOME_SEARCH_VEL =                -.50
HOME_LATCH_VEL =                 .10
HOME_USE_INDEX =                 NO
HOME_IGNORE_LIMITS =            YES
HOME_IS_SHARED = 		 1	
HOME_SEQUENCE =			2

#+ Second axis
[AXIS_1]

TYPE =                          LINEAR
HOME =                          -1.000
MAX_VELOCITY =		0.275
MAX_ACCELERATION =              1.5
STEPGEN_MAXVEL =        0.3025
STEPGEN_MAXACCEL =              1.65
BACKLASH = 0.000
INPUT_SCALE =                   28800
OUTPUT_SCALE = 			1.000
 MIN_LIMIT =                     -24.0
 MAX_LIMIT =                     0.10
FERROR = 			0.050
MIN_FERROR = 			0.010
HOME_SEARCH_VEL =                .50
HOME_LATCH_VEL =                 .10
HOME_USE_INDEX =                 NO
HOME_IGNORE_LIMITS =            YES
HOME_IS_SHARED = 		 1	
HOME_SEQUENCE =			1

#+ Third axis
[AXIS_2]

TYPE =                          LINEAR
HOME =                          -1.0
MAX_VELOCITY =		0.275
MAX_ACCELERATION =              1.5
STEPGEN_MAXVEL =        0.3025
STEPGEN_MAXACCEL =              1.65
BACKLASH = 			0.000
INPUT_SCALE =                   28800
OUTPUT_SCALE = 			1.000
MIN_LIMIT =                     -6.0
MAX_LIMIT =                     0.1
FERROR = 			0.050
MIN_FERROR = 			0.010
HOME_OFFSET =                    .010
HOME_SEARCH_VEL =                .50
HOME_LATCH_VEL =                 .10
HOME_USE_INDEX =                 NO
HOME_IGNORE_LIMITS =            YES
HOME_IS_SHARED = 		 1	
HOME_SEQUENCE =			0


###############################################################################
# section for main IO controller parameters 
###############################################################################
[EMCIO]

#- Name of IO controller program, e.g., io
EMCIO = 		io

#- cycle time, in seconds
CYCLE_TIME =            0.100

#- tool table file
TOOL_TABLE =            stepper.tbl