Cheers Guys for your feedback.
I will try and swap the wires.
The firmware update seems easier, but will have to remind myself to do it every time I update firmware.
This patent of Stratasys is a good guide when building a heated build chamber:
http://www.google.com/patents/US6722872
It says that the heated chamber really should be between 70-90 degC for ABS and all the steppers etc should be outside of it.
I reckon that the uM is idealy made to convert to this, apart from the structure being made of wood.
Just swap the motors to the outside and all that is really left is to make sure that the bowden tube gets cooled.
Perhaps wrapping insulation around it plus blowing cooler air into the tube would work.
Ideally the PCB underneath should be transferred to the back with some insulation in between.
Quick fix obviously is a heated bed, but seems to me that that is only half of the solution..