Best way to get dimensionally accurate parts using Slic3r

So I have a MakerFarm Prusa i3 8" printer. I normally use Slic3r for my slicing needs. I recently became curious about how accurate my printer will print parts. So I made a simple test square to see how far off (or ow close) my printer prints. In SketchUp I made my test square 1" x 1" x .25" thick. In the middle of the square I put a 1/2" hole. In previous tests the 1/2" hole measured 0.030" smaller than my desired .500". In this test square I compensated for that and enlarged the hole by 0.030". As you can see by the picture, the dimensions are relatively close, yet there are some discrepancies. Any ideas on what I should do to avoid having to enlarge holes by 0.030" just to get them the I want?

Oh, and here are my Slic3r configs. Thanks for the help in advance!

# generated by Slic3r 0.9.9 on Tue Mar 18 19:30:03 2014
avoid_crossing_perimeters = 0
bed_size = 200,200
bed_temperature = 0
bottom_solid_layers = 3
bridge_acceleration = 0
bridge_fan_speed = 100
bridge_flow_ratio = 1
bridge_speed = 60
brim_width = 0
complete_objects = 0
cooling = 1
default_acceleration = 0
disable_fan_first_layers = 1
duplicate = 1
duplicate_distance = 6
duplicate_grid = 1,1
end_gcode = M104 S0 ; turn off temperature\nG28 X0 ; home X axis\nM84 ; disable motors
external_perimeter_speed = 70%
external_perimeters_first = 0
extra_perimeters = 1
extruder_clearance_height = 20
extruder_clearance_radius = 20
extruder_offset = 0x0
extrusion_axis = E
extrusion_multiplier = 1
extrusion_width = 0
fan_always_on = 0
fan_below_layer_time = 60
filament_diameter = 3
fill_angle = 45
fill_density = 0.4
fill_pattern = honeycomb
first_layer_bed_temperature = 0
first_layer_extrusion_width = 200%
first_layer_height = .2
first_layer_speed = 30%
first_layer_temperature = 200
g0 = 0
gap_fill_speed = 20
gcode_arcs = 0
gcode_comments = 0
gcode_flavor = reprap
infill_acceleration = 0
infill_every_layers = 1
infill_extruder = 1
infill_extrusion_width = 0
infill_first = 0
infill_only_where_needed = 0
infill_speed = 60
layer_gcode =
layer_height = .4
max_fan_speed = 100
min_fan_speed = 35
min_print_speed = 10
min_skirt_length = 0
notes =
nozzle_diameter = 0.4
only_retract_when_crossing_perimeters = 1
output_filename_format = [input_filename_base].gcode
perimeter_acceleration = 0
perimeter_extruder = 1
perimeter_extrusion_width = 0
perimeter_speed = 30
perimeters = 5
post_process =
print_center = 100,100
raft_layers = 0
randomize_start = 0
resolution = 0
retract_before_travel = 2
retract_layer_change = 1
retract_length = 1
retract_length_toolchange = 10
retract_lift = 0
retract_restart_extra = 0
retract_restart_extra_toolchange = 0
retract_speed = 30
rotate = 0
scale = 1
skirt_distance = 6
skirt_height = 1
skirts = 2
slowdown_below_layer_time = 30
small_perimeter_speed = 30
solid_fill_pattern = rectilinear
solid_infill_below_area = 70
solid_infill_every_layers = 0
solid_infill_extrusion_width = 0
solid_infill_speed = 60
start_gcode = G28 ; home all axes\nG1 Z5 F5000 ; lift nozzle
support_material = 0
support_material_angle = 0
support_material_enforce_layers = 0
support_material_extruder = 1
support_material_extrusion_width = 0
support_material_interface_layers = 0
support_material_interface_spacing = 0
support_material_pattern = rectilinear
support_material_spacing = 2.5
support_material_speed = 60
support_material_threshold = 0
temperature = 200
threads = 2
toolchange_gcode =
top_infill_extrusion_width = 0
top_solid_infill_speed = 50
top_solid_layers = 3
travel_speed = 130
use_relative_e_distances = 0
vibration_limit = 0
z_offset = 0

Slic3r puts the print head path on the actual circle of the hole, so the actual hole is smaller by the width of that extruded plastic in each direction. Skeinforge has a setting for automatically enlarging holes to compensate for this (though I've only looked through the mass of skeinforge controls and never actually used it!) Slic3r doesn't have an option for this (that I've found)

The rest of the dimensions look pretty good. My prints are always very slightly under height because I smush the first layer down pretty hard to get good adhesion on the bed. I'm sure if I tuned that up more accurately I could get better results but the error isn't big enough to be important at the moment.