Lower the bike if it is for safety and stability reasons...just do it a little at a time...but both ends and consult with Progressive or the maker of the shocks/kit, keeping in mind what you are going to be using bike for solo or two-up, lightly or heavily laden...!
As the ground clearance will suffer, you have to be more careful with low hanging hardware like the floorboards and such, may also have to tuck things inboard a bit to get some more lean angle. Being slight of build, I HAD to lower the bike, and yes I had to select accessories likes pipes, pegs/floorboards and modify mounting bracket/hardware and bumper for side stand and file a bit of it flat to gain more lean angle.