I've had the same exact issues with harshness as you and am curious about the answers you get. So far I've also gone from "off the shelf" Fortune Auto 510s to KW V3s and honestly the ride isn't much better/different regardless of settings and I've tried tons of combinations of bump and rebound settings. I can get them to the point of being underdamped but they still feel harsh.
I recently lowered the springrates on the V3's from 8k/9k to 6k/7k and they're a tiny bit better but still relatively harsh. I also have nismo bushings pretty much everywhere besides the subframe (I have collars) and SPC front tension rods with rubber bushings. Short, abrupt bumps and dips (like tree roots under the road) are the worst and I wonder if it's tied to high speed damping on all shocks made for our cars.