The wire inside the cowl is an auxillary power supply connection for attaching a lighting system to the powerchair. It has 24VDC available, and it does not connect to anything for normal operation of the chair.
The lights flashing constantly indicate that the joystick is out of position, or you are in neutral, or the chair is plugged into the charger, if it is a constant flash. Take it off the charger, place it in drive and keep hands off the joystick and restart. If it is still flashing, try a restart, then immediately press the "horn" button twice. If still no-go, you'll need a tech to look at it as the controller may be bad, or the joystick.
If it is a patterned flash, like 4 times flash, pause, repeat, then the onboard computer has found a fault. The number of flashes specify the fault, (right motor, left brake, etc.) go to the CTM website here to download the owners manual which show the flash codes.
http://www.ctmhomecare.com/About_Us/index.asp?tStyle=01