You will definitely feel that side to side vibe at idle and up to about 2000RPM. Beyond that, you probably need a carb balance.
Those twin disks should work very well. If you have the original rubber brake hoses, replace them with some quality braided stainless. Speigler makes a pretty nice kit, that includes the line for the rear disk as well. Change out the original fluid and reverse bleed the system. You will find a HUGE difference. Won't be as good as some of the new bikes, but will definitely improve over the stock OEM setup.