I'm guessing your ship is pretty tall. Connect 6-symmetric struts from a wide point near the middle to the highest point on the craft you can. this will help keep it rigid. It's OK if the struts connect parts from separate stages. they will automatically disconnect. Try putting 4-symmetric canards at the highest possible point. They will be dead weight for the rest of the mission, but they work wonders for stabilizing tall rockets. Also, whenever you have stages connected to the sides, go ahead and use struts to connect the side stages to eachother at the top and bottom, and connect them to the main rocket at at least one place. SAS will be most effective in the middle of the rocket. Try using two or three SAS modules.