I've been searching the forums for a DIY on parts that are factory installed to pass vehicle inspection off the production flirt that can be removed. I apologize if there is a thread and I'm duplicating it. I have a 06 S2R, thanks in advance.
Common mods would be to change the exhaust. I believe your bike came with a catalytic converter as well. That could be swapped out for different headers.
You could remove the blinkers.
Many folks with early Monsters would remove the rear fender, guard, then cut the rear loop off the frame. They make plastic plugs and aluminum plugs to fill the void in the tubing. Ducati Monster Tail Chop . Com offers easy plate and brake light relocator kits.
Rear passenger pegs.
Front sprocket cover.
Of course it's all dependent upon where you live, your local laws, codes and ordinances, as well as what you plan to do with the bike as far as riding it.