I would echo the comment on not needing upgraded brakes for our sport, on that bike's projected speeds at least. I suppose the argument that could be made, not necessarily in your case, would be visible reduction of the weight of the hardware.
As for the exhaust mods, all the visible dimensions, especially the rear opening are factory. Internal mods, such as baffle mods, are allowed and were recommended to me by two of the techs. Since they led me down that path, I would have been quite irritated if I couldn't work them back to passable. My wallet would have appreciated leaving the welds visible. Actually that whole effort had minimal value with the core of the motor being stock
As to painting, alot of folks are running production class with non-stock paint jobs; however, in this particular case, the black exhaust was offered by the factory and matches up with manual photos.