If you've got to repaint a V-Strom, there's only one choice:
Bedliner! 
Though I have to say, I love that dark blue that the '05s came with. I wish mine were that color, but I took what I could get at the time: red.
But if you're intent on getting it back to stock, then absolutely, just get a new part. I wouldn't mess with repainting unless new parts were no longer available. The V-Strom is still in production, so the parts are out there. Make it easy on yourself.
