There is rather a bit more to your shifter linkage than it would seem. Part of how it works in practice is the ergonomics of your foot peg and foot. On the other end, the mechanics of how the shifter mechanism (inside the transmission case) on any particular bike make comparing bikes directly impractical. On your bike, the shift pedal lever is quite long and the shaft it rotates on is actually behind the peg. It takes a fairly large amount of torque to operate the transmission which is ok because you have the leverage with the long pedal. Compare to a factory bike with a linkage like a CB400F. That bike has a very short pedal, and the crank arms are very short, parallel, and with some pretty sloppy rod ends to boot. Works fine on the Honda, but you would find it miserable if not impossible on the Yamaha. Why? Because the transmission itself takes greatly less force to rotate the mechanism. You can't conveniently alter the RD's transmission, but you can replicate the stock pedal's action and locate it in a different spot.
First, consider the difference in pedal length. If it took 10 lbs of pressure to select a gear with the stock pedal, and your new pedal is 75% as long, it now takes 13.3 lbs of pressure to do the same job. That is a big difference. With the same amount of rotation, the throw is shorter with the shorter pedal. So you trade throw for power. Longer pedal = longer throw = less effort. You can make up for this by adjusting the lengths of the two crank arms. If the driving arm is shorter, it will deliver more force than a longer arm. Keep in mind that this is the opposite situation of the pedal. There the leverage of the pedal applies a torque to the shaft. For the driving crank arm, the torque of the shaft results in force at the end of the arm. For example, if you you start with a 12 inch pedal and apply 10 lbs to it, you get 120 in-lbs of torque. If you have a 4" crank arm, 120 in-lbs/4 in = 30 lbs of force, and if the driven arm on your shifter shaft is also 4", you get 30 lbs x 4" or 120 in-lbs of torque again. So you get the same torque with the linkage as with just the direct connect pedal. But if you shorten the pedal to 9" you only get 90 in-lbs of torque with the same 10 lbs of foot pressure. To get the needed 120 lbs of torque, you need to add another 3.3 lbs. However, shorten the driving crank arm to 3" and you get 90 in-lbs/ 3 = 30 lbs of force, and when that is applied to the 4" crank arm on the shift shaft, you get back the originally needed 120 in-lbs of torque. So to maintain the same torque with a linkage, the crank arm lengths must have the same ratio as the change in pedal lengths. In this case, the 9" pedal is 75% as long as the 12" original, and the driving crank arm of 3" is 75% as long as the driven arm of 4".
Unfortunately, there is a problem. This situation ONLY happens when the crank arms are both parallel AND at 90 degrees to the connecting link. Consider the driving crank arm on a linkage with the connecting link above the pedal and shift shaft (like J-rods Honda in the previous post): At 90 degrees, the arm offers the least effort on the link. As the arm rotates clockwise, and the angle becomes less and less than 90 degrees, the force delivered to the link increases due to the inherent mechanical advantage. Similarly, the driven arm sees less and less effort applied to it as the angle between it and the link increases past 90 degrees. In a same length 90 degree parallel crank arm scheme these effects cancel out, but changing the arm lengths and their angles with the link can have a very noticeable effect on the performance.
This gets rather complicated, so consider it from a more basic perspective. Lets say you have your linkage built like the above example, 9" pedal, 3" driving crank and 4" driven crank. The crank arms are parallel, and at 90 degrees to the connecting link when the system is at rest. Assuming the transmission shifts equally easily for upshifts as well as downshifts, the linkage will also apply equal force for upshifts as well as downshifts. When you ride the machine, you find it is easier to downshift. Why? Probably because it is physically easier to apply more force down on the shift pedal than it is to lift it up. Here is one possible adjustment that will help the situation. Remove the driven crank from the shaft and rotate it one spline counterclockwise and lengthen the connecting link to match. Now the angle between the driven crank arm is less than 90 degrees. The angle between the driving arm and the link is still 90 degrees. When you lift up on the shift pedal, the driving arm delivers more linear force the more acute the angle with the link becomes. The driven crank arm on the other hand, has changed. Instead of the torque decreasing as the angle becomes greater than 90 degrees, the torque INCREASES as the angle gets closer and closer to 90 degrees. Maximum torque is achieved at 90 degrees. So upshifting is easier, and downshifting is harder. There is never a free lunch though, anything that gets you needing less effort gets paid for with greater travel or throw.
There is a great deal more to all this but hopefully this hits the high spots. I used to think quality rod ends/bushings/bearings was important. The shorter the crank arms, the greater the impact of sloppy joints. Slop in joints/bearings is fixed, and longer arms result in less rotation required to take up any slack. That said, sloppy joints (up to a point) is irrelevant for how well the system works. Even ridiculously sloppy setups seem to work great as long as there is no binding. Evidently your foot takes up all the slack and the trans can't tell the difference.
And finally, one last thing to consider: Your ankle rotates your foot on an axle that is in a different location than the axle your pedal rotates on. It has an effect on how you perceive the operation of your shifter.
