I have far more respect for short riders that don't go the way of lowering a bike to feel comfortable. I'd far rather see them learn to get one solid foot down on one side or the other than to have to rely on a shaky position where they are barely touching on either side. I don't care what you say, I've heard it all, LOWERING A MOTORCYCLE, even if you do the front and back equally, WILL AFFECT THE HANDLING!!!!
Or for God's sake, at least put the bike back to stock after you become a comfortable enough rider that you don't need to have both feet down. All it requires is that you be a little more competent at low speeds and a little more careful where you stop and where you park.