I'm very active on the S40 forum, the bike which my cafe racer is built upon. This is a cut-n-paste from a series of suspension upgrade and tuning articles that I have written for that forum. It has been edited/adapted for FZ6 purposes.
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Damping Rod forks are a fairly simple design with few parts - that's why they are used on budget bikes. The damping rod is a tube with an opening on the top and a pair of small holes on the lower portion of the tube. The damping rod has a seal that acts as a piston as the slider moves up and down the fork tube. As the fork is compressed the piston moves/forces oil through the damping rod from the top of the tube through the smaller holes on the bottom. This creates resistance inside the fork itself. This resistance to movement is called damping; compression damping as the fork compresses and rebound damping as the spring in the fork seeks its static or neutral position.
How did Yamaha select the rate of the spring and the size of the holes in the damping rod? They estimate an “average rider” across their vast market. In this case a rider who weighs around 150-160 pounds. If this is you, your springs have been designed with you in mind. If this is not you, your bike is most likely under-sprung for you. Also, you may weigh 160 pounds, but you have added equipment and accessories to the bike that increased its weight. If this is the case, the combined weight of the bike, accessories and you are now outside the design limit of the springs.
The limiting item in the FZ6 forks is the damping rod itself. It offers zero tunability. Damping rods are inexpensive to manufacture but have significant limitations. As noted above, to create compression damping, oil is forced through the holes at the bottom of the damping rod. Forcing oil through a hole creates very little resistance to flow at low speed, such as hitting a dip or gully or applying the front brakes. This allows the forks to shoot through their travel fairly easily, diving or bottoming in these situations. On the other hand when the wheel hits something fast or sharp edged (like a pothole) it needs a lot of oil to pass through the damping holes very quickly. Unfortunately the nature of forcing oil through a hole is that as the wheel velocity increases the damping force increases with the square of the velocity. In other words if you double the velocity you get four times the force. This means the hole basically "hydraulic locks" resulting in a harsh or stiff ride. Damping rods give the worst of both worlds; they are both too mushy and too harsh at the same time. The use of progressive rate fork springs further complicate this this because they amplify these undesirable performance characteristic.
There aren’t many “easy” or inexpensive solutions here. The inexpensive solution that many try is to use higher viscosity oil. While this will improve damping during slow-speed events, the forks will hydrolock sooner during high speed events. For this reason I don’t suggest this approach. One could experiment with increasing the size of the holes at the bottom of the damping rod AND using heavy weight oil, but this more than likely would be a zero sum gain. The only real solution to improve the damping of the forks is to use a cartridge emulator that bypasses the holes in the damping rod, replacing their function with a spring actuated valve that provides dynamic damping.