Here is the code I use for the right extruder only.
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; **** Replicator 1 dual start.gcode ****
M103 (disable RPM)
M73 P0 (enable build progress)
G21 (set units to mm)
G90 (set positioning to absolute)
M140 S[bed0_temperature] T0 (set HBP temperature)
(**** begin homing ****)
G162 X Y F2500 (home XY axes maximum)
G161 Z F1100 (home Z axis minimum)
G92 Z-5 (set Z to -5)
G1 Z0.0 (move Z to "0")
G161 Z F100 (home Z axis minimum)
M132 X Y Z A B (Recall stored home offsets for XYZAB axis)
(**** end homing ****)
G1 X-110.5 Y-72 Z50 F3300.0 (move to waiting position)
G130 X20 Y20 A20 B20 (Lower stepper Vrefs while heating)
M134 T0; (wait for hotbed)
M104 S[extruder0_temperature] T0 (set extruder temperature)
M133 T0 (wait for toolhead and HBP to reach temperature)
G130 X127 Y127 A127 B127 (Set Stepper motor Vref to defaults)
M108 T0
M135 T0
G0 X-113 Y-72 (Position Nozzle)
G0 Z0 (Position Height)
G92 E0 (Set E to 0)
G1 E6 F300 (Extrude 6mm of filament)
G92 E0 (Set E to 0 again)
G1 X-110 Y-65 F300; (Slow wipe)
G1 Z0.6; (Raise back up)
M73 P0 ;@body (notify GPX body has started)
; **** end of start.gcode ****
I changed it from the makerware defaults to just extrude some plastic on the edge instead of making a long strip of plastic across the front. I've been using this for some time and have been satisfied enough not to change it for a while.