The WBO2/Aux. harness colors are different for everyone, so you can't go by color.
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Yes you can flash without it installed. Assuming you're using the built-in serial connector on the blackbox, only the power cord needs to be hooked up. The tricky part is when you click UPLOAD on the flash program, you have less than 2 seconds to power up. You will know you're successful when it is flashing for 17 seconds, and then verifying for another 17 seconds.
Instead of powering up with the power cord provided, I use a 7 to 15 volt DC power adapter. Make sure the plug provides ground on the outside, and voltage on the inside.
If you want to flash using the other serial port (ie serial cable), you must insert the rotary encoder and hold it down. When the LCDBC is first powered up if it sees the rotary encoder pushed down, it will switch serial ports. You can let go of the rotary encoder once flashing process begins.
EDIT: I must have read over this 4 times.
For anyone else wondering " Boost solenoids are not polarity sensitive so it does not matter which wire goes to
which"
So before I solder these together. These wires and connect which ever way?
http://i.imgur.com/sprfe.jpg