Does anyone know how much it would cost to repair some scratches and paint fairings (upper and lower left side)? The scraches are pretty bad. I'm wondering if it will be cheaper to buy new ones or fix mine.

depends on the scratch and which panel you need.
Generally repairs in the abs plastic look like crap. Any wreck I've ever put back together gets new plastic. Save the rashed stuff for the track. You can check out ebay, or if you know the yamaha part numbers check out www.cycle-parts.com they have the cheapest OE parts around.

I think you should just man up and buy some special edition fairings