I agree, just loosing the seat, bags, and changing the handlebars will make a world of difference. Some nice subtle changes would be to get rid of the reflectors and change out your blinkers, tail/brake light, change out the pipes, maybe throw a nice coat of paint on it. A small fairing on the front will help with the "look" and a low 2-up seat will help slim it out while keeping its functionality. Just tossin some ideas around!
But first, like everyone says, get her running and running right. Then dick with cosmetics. Good luck and have fun with it!