GONZO X I would think any bike left out in the rain and elements would start to rust a bit. Is it covered at all? Naval jelly.jpg
To neutralize it get a bottle of Naval Jelly. It turns the rust invisible fast. Make sure you can wash it off with soap and water and use fine steel wool to get them spokes shiny again, then wax em.
Sun and weather take a toll on Motorcycles fairly fast. You just need to do extra detailing. The clear coat problems sound odd. Post a picture if you can. These things would be pretty easy to paint, even with a rattle can and some clear coat once the prep sanding and primer were applied.