Cupcake No Extrusion

[CMDann]

Hey there, I know this is old and likely dead but thought I would ask. When I connect my cupcake CNC to my computer and run generate the gcode, it includes the start gocode you would expect:

(**** beginning of start.gcode ****)
(This file is for a MakerBot Cupcake CNC with a Heated build platform)
M104 S220 T0 (Extruder Temperature to 220 Celsius)
M109 S110 T0 (Heated Platform Temperature to 110 Celsius)
M107 (fan off)
G21 (Metric FTW)
G90 (Absolute Positioning)
G92 X0 Y0 Z0 (You are now at 0,0,0)
(You have failed me for the last time, MakerBot)
G0 Z15 (Move up for warmup)
M108 S255 (Extruder speed = max)
M6 T0 (Wait for tool to heat up)
G04 P5000 (Wait 5 seconds)
M101 (Extruder on, forward)
G04 P5000 (Wait 5 seconds)
M103 (Extruder off)
M01 (The heated build platform is heating up. Wait until after the lights have turned off for the first time, clear the test extrusion, and click yes.)
G0 Z0    (Go back to zero.)
(**** end of start.gcode ****)

This particular line doesn't seem to work, ie: the popup never comes up: M01 (The heated build platform is heating up. Wait until after the lights have turned off for the first time, clear the test extrusion, and click yes.). I have tried manipulating this, as even if I remove those lines the motors work fine but the motor does not extrude at all.

I have changed my start gcode to this:

(**** begin initilization commands ****)
G21 (Metric FTW)
G90 (Absolute Positioning)
M108 S255
M104 S220 T0 (Temperature to 220 celsius)
M109 S110 T0 (set heated-build-platform temperature)
(**** end initilization commands ****)

But that still doesn't work. I am able to manually extrude the machine through the control panel just fine. I am also able to move the steppers. I think the problem is the gcode is being generated for a stepper motor and I seem to be using an older plastruder that uses an RPM command (not sure).

Here is a small album showing the machine and manually extruding: http://imgur.com/a/PaFI4

Also a link to my question on Reddit: https://www.reddit.com/r/3Dprinting/comments/4g5i8z/help_with_old_printer/

I do realize this is an older machine but I am trying to get it working for educational use and to add to a small makerspace with a tight budget.

Thanks 🚀

[CMDann]

I should also add I have tried this all on Replicatorg 40, using Skeinforge 35+ and I have tried it on Windows, Mac, and Linux.