Sounds like a damper issue to me. You are having to soften the Tokicos, which have very stiff compression damping, a lot in order to be comfortable. However, given the "bounciness", this says that the spring rate/damper combo is now very underdamped, meaning that the damper has less control of the spring/mass.
A damper with relatively stiff low-speed damping but softer high-speed damping should still perform well, while riding better. I'm hoping to find a damper that can accomplish this and accomodate a Z coilover install as well, as my Z has Eibachs/HPs now which ride rough and have very little bump travel before the ES poly bumpstop (which I haven't cut, yet).
The nicer bump stops should help too, if you hit them often. Just take a look at a bumpstop some time and it will be pretty obvious whether you're been riding them or not.
A lower unsprung/sprung weight ratio will improve ride and generally decreasing unsprung weight (wheels, tires, brakes, some suspension parts, etc.) will have a positive effect on ride, handling, acceleration, braking and traction.