I think I know what your biggest problem is: you are in profile 6, which is meant for brushed motors only(!); but you've got a brushless motor hooked up. You said:
erm, All 4 LEDs light up, then each they all flash 6 times. Then they individually light up in turn then it goes back to red and green perminant.
When all four lights are flashing, its informing you of the profile you are in. Profile 6 is for brushed motors, not brushless. Find the instructions about the profiles here
Unfortunately, it looks like you might have damaged the speed controller; Novak warns you to never connect a brushless motor when the speedo is in brushed mode (profile 6). You can try to change it back to brushless mode by doing the following:
1. Turn the speedo off.
2. Remove the sensor wires from the speedo.
3. Press and hold the set-up button.
4. Turn the speedo on (while still holding the set-up button!).
5. When the blue and red LED's come on, release the set-up button.
6. The blue and red LED's will flash 9 times and then go solid.
7. When the blue and red LED's are solid, quickly press and release the set-up button.
8. The green LED will flash for a few seconds; after that turn the speedo off and reconnect the sensor wire.
Go ahead then and hook it back up and try it out. Hopefully it will work for you, if not you'll probably need to talk to Novak.