I don't know why it annoys me but there is a wire floating around behind the air filter on the blackline 

Does anyone have any idea what it was / should be connected to?

It may be for anti pollution etc, a sensor that may have been in the original air filter housing?
tape it up and make sure you cover the contact points so water / dust doesnt get in as it may throw errors on the ECM

Yeah the bike starts and runs great so I don't think it is important but never thought of sealing it up, good idea thanks. 

Looks like a plug for the active air intake. Connects at the back of the stock air cleaner and opens a flap under WOT. Is your A/C stock? 

I don't know if a/c is stock although I have seen the same one on a lot of pictures of blacklines and I haven't pulled the cover off.

Got the same on my Rocker.

just tape off & zip tie up out of the way

That's a great idea since we are getting into the wet time of year. 

could also slip a  little dielectic grease in the pin holes to help prevent corrosion if a little moisture gets in.