"There's a flashing red R just below where it says MDI."
This means that G0 is active. In the MDI field, type G1 and flashing row R will go off.
"However I can jog left / right and back / forward but the X axis will not go up, it will only go down and is almost touching the baseboard now."
Do you mean the Z axis?
When you look at the machine from the front and press:
- "Y-" the gantry should move from you
- "Y +" the gantry should move towards you
- "X-" the spindle should move to the left
- "X+" the spindle should move to the right
- "Z-" the spindle should move down
- "Z+" the spindle should move upwards