Scramblers are having problems with the spokes on the rear wheel breaking, hitting the swingarm or brake caliper, and puncturing the tube. Make sure to check the spoke tension often. Safety-wire the spokes together where they cross to keep a loose spoke from flailing about, and use several layers of duct tape instead of a rim strip to protect the tube in case a spoke does break. Carry spare spokes.
My plan would be an aluminum box on the left, a solo seat with luggage rack instead of the pillion, a Givi top box on that, and the factory luggage rack that goes over the rear fender (behind the stock seat) behind that. Don't put a bag on the right side at all. (The exhaust system weighs a lot, so a bag on one side will be fine if you don't overload it too much)
I'd also install a tank bag and some cloth panniers that hang down on either side of the gas tank. Finish it off with a small windshield and some hand guards.