Ok since there aren't any pic's of what you have I'll just wing it.
I'm assuming you have a flat lens for the signal and you will need to mount the leds to a circuit board or something similar. I would drill 2 holes in the lens as close to the opening on the bike as possible. Doing this will allow the lens to stay in place without having to drill into the fairings. This way if you decide later you don't like it you don't have holes to cover up. Then get some screw spacers short enough to get the leds close to the lens. You could use drywall anchors for this. Then drill 2 matching holes in the circuit board. You will also need to seal the whole thing from the elements so some type of box to cover the whole assembly will be needed.
Going off of your description this is what I came up with.
hope this helps