Thank you for the replies.
For some reason I'm not seeing the button for attaching a file, so I'm going to paste my motenc.ini file in here. I'm finding I have to specify MAX_ACCELERATION at 80 in/sec/sec in order to actually get 40 in/sec/sec.
# 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.
# General section
[EMC]
# Version of this INI file
VERSION = $Revision$
# Name of machine, for use with display, etc.
MACHINE = LinuxCNC-MOTENC
# Debug level, 0 means no messages. See src/emc/nml_int/emcglb.h for others
#DEBUG = 0x00000003
#DEBUG = 0x00000007
DEBUG = 0
# Sections for display options
[DISPLAY]
# Name of display program, e.g., tkemc
DISPLAY = tkemc
#DISPLAY = axis
# Cycle time, in seconds, that display will sleep between polls
CYCLE_TIME = 0.0500
# Path to help file
HELP_FILE = tklinucnc.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 = 1.5
# Prefix to be used
PROGRAM_PREFIX = /home/robert/linuxcnc/nc_files/robert_gcode_files
# Introductory graphic
INTRO_GRAPHIC = linuxcnc.gif
INTRO_TIME = 5
# Task controller section
[TASK]
# Name of task controller program, e.g., milltask
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 = motenc.var
# Motion control section
[EMCMOT]
EMCMOT = motmod
# Timeout for comm to emcmot, in seconds
COMM_TIMEOUT = 1.0
# Interval between tries to emcmot, in seconds
COMM_WAIT = 0.010
# Servo task period, in nanoseconds
SERVO_PERIOD = 1000000
# 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_servo.hal
HALFILE = motenc_motion.hal
HALFILE = motenc_io.hal
# rwp add 6/1/14
HALFILE = axisWatch.hal
# rwp add 7/2/16
HALFILE = handwheelFile.hal
# list of halcmd commands to execute
# commands are executed in the order in which they appear
#HALCMD = save neta
# Trajectory planner section
[TRAJ]
AXES = 3
# COORDINATES = X Y Z R P W
COORDINATES = X Y Z
HOME = 0 0 0
LINEAR_UNITS = inch
ANGULAR_UNITS = degree
CYCLE_TIME = 0.010
DEFAULT_VELOCITY = 3.0
MAX_VELOCITY = 4.0
DEFAULT_ACCELERATION = 6.
MAX_ACCELERATION = 80.
# Axes sections
# First axis
[AXIS_0]
TYPE = LINEAR
HOME = 0.000
MAX_VELOCITY = 4
MAX_ACCELERATION = 80.0
BACKLASH = 0.000
INPUT_SCALE = 10160
OUTPUT_SCALE = 10
OUTPUT_OFFSET = 0
MIN_LIMIT = -25.03
MAX_LIMIT = 0.03
FERROR = .2
MIN_FERROR = .020
HOME_OFFSET = 0
HOME_SEARCH_VEL = 0
HOME_LATCH_VEL = -5
HOME_USE_INDEX = YES
HOME_IGNORE_LIMITS = YES
MAX_OUTPUT = 1
# PID tuning params
DEADBAND = 0.000015
P = 50
I = 0
D = 2
FF0 = 0
FF1 = 0
FF2 = 0
BIAS = 0
# Second axis
[AXIS_1]
TYPE = LINEAR
HOME = 0.000
MAX_VELOCITY = 4
MAX_ACCELERATION = 80.0
BACKLASH = 0.000
INPUT_SCALE = 10160
OUTPUT_SCALE = 10
OUTPUT_OFFSET = 0
MIN_LIMIT = -24.53
MAX_LIMIT = 0.03
FERROR = 0.2
MIN_FERROR = 0.020
HOME_OFFSET = 0
HOME_SEARCH_VEL = 0
HOME_LATCH_VEL = -5
HOME_USE_INDEX = YES
HOME_IGNORE_LIMITS = YES
MAX_OUTPUT = 1
# PID tuning params
DEADBAND = 0.000015
P = 50
I = 0
D = 2
FF0 = 0
FF1 = 0
FF2 = 0
BIAS = 0
# Third axis
[AXIS_2]
TYPE = LINEAR
HOME = 0.0
MAX_VELOCITY = 4
MAX_ACCELERATION = 80.0
BACKLASH = 0.000
INPUT_SCALE = 10160
OUTPUT_SCALE = 10
OUTPUT_OFFSET = 0
MIN_LIMIT = -8.03
MAX_LIMIT = 0.03
FERROR = 0.2
MIN_FERROR = 0.199
HOME_OFFSET = 0
HOME_SEARCH_VEL = 0
HOME_LATCH_VEL = -5
HOME_USE_INDEX = YES
HOME_IGNORE_LIMITS = YES
MAX_OUTPUT = 1
# PID tuning params
DEADBAND = 0.000015
P = 50
I = 0
D = 2
FF0 = 0
FF1 = 0
FF2 = 0
BIAS = 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 = motenc.tbl