Mate, I've ridden with everything on my SD from the standard bars to Rizoma straight ones, LSL flat bars and now clip-ons.
IMO if the roads your riding on and the speeds you're doing are resulting in a bit of head shaking over crests and maybe uneven surfaces then this is totally normal for the SD. This is why the SDR has a damper and they revised the steering geometry a bit from the '06 model, (which is even more twitchy).
If you put on the standard bars, (which are pretty high and make you sit up with less weight over the front), then it will make it even more light on the front end and prone to wheelying and shake.
I'd just get on and enjoy the feeling. After a while you get to trust the frame and suspension to sort out the wobble and you just get to know the feeling when it goes light and shakes a bit. Or slow down on crests a bit!
I have a Scotts damper and it's so good and so adjustable on the fly that I haven't had a shake or wobble in three years.