Hi 2 part question 

Just changed over my flat battery. Putting things back into place and I noticed what look like a fuel breather line coming from the rear of the tank? Does this sit freely or is it plugged into something ? I can't find where it may lead to. 

Also seems as though the clips that hold the battery cover in place is a little worn. It won't hold the cover in place anymore. Just keeps falling off. I thought maybe some wires may be pushing it out but I took the clips off the bike and it Clearly doesn't lock into the battery cover anymore. 

Anyone experience this?

The clips are a common problem. I have replaced one with a nice hidden cable tie which can be re-used. That battery cover isn't going anywhere now. You can buy the clips from ebay/harley if you want, but a hidden cable tie is all you need.

Thanks mate. I've managed to zip tie it nice and neatly. It will do for now. I can still access the battery charger clips without taking the cover off also.
I'm glad it's a common problem in a way

No problem. I also have my battery charger routed and tucked in under the seat, so only have to take the seat off if I want to connect the charger. Much quicker.

A trickle charger with an always attached (to the battery) plug would be way easier... You don't have to take off anything that way.

The whole charger attached? I have the plugs connected to the battery which stay under the seat. I can take the seat off and plug the charger cable to the other part of cable which connects to the battery. 

Aha! Yep I have the similar cable, but might look at a way to discretely route it so I don't have to take the seat off.