Adjusting the STV (secondary throttle valve) has shown to make a difference in the RPM range from just above 1500 to just below 4000. The engine runs smoother and seems to have better response. Also some have reported better fuel mileage and a linier throttle response.
There are two different methods for synchronizing the secondary throttle valves. These procedures will work for both the 1000 and 650 models. Please note that the 650 adjusts from the rear throttle body and the 1000 from the front throttle body.
To access the linkage and adjusting screw, remove the tank and entire air cleaner housing. While there, also check the clamps for the throttle bodies as they have been found loose from the factory.
The valve plates sit slightly open with the engine off. Grabbing the linkage by hand and close the plates, you may notice that the plates are not open the same amount; this is what you are adjusting. By turning the screw just above the TBS screw, the front plate can be moved to more open or closed. The back cylinder is the constant.
There are two ways to measure the difference between the secondary throttle plates.
The first method, is to use a small piece of wire like a spark plug gap checker that is made of different size wires bent in a small "L" shape. Take a pair of pliers and straightened out a few of the smaller ones. Try the .020, .024, .028, .032. Then try inserting the wire between the throttle plate and the air horn while holding the linkage in the closed position. Adjust the screw so that the gap is the same for the front and rear plates. As the gap becomes closer you will need to use different size wires.
The second method is to measure the height of the open side of the throttle plate to the top of the air horn. For this, you will need a depth gauge that can measure very small increments. Adjust the screw so that the front and rear plates are the same measurement down from the top of the air horn while holding the linkage closed.
After the adjustment is made, be sure to paint the adjusting screw so it will not move from vibration. This can be done with nail polish.
Either method will work, it is thought that the second method is the more accurate.
After reassembly, you will need to perform a TBS (throttle body synchronization).
Don't grab the 650 plates and try to move by hand, can't be done without damage. The nut circled in red, in the first photo below, is turned by hand to move the secondary plates. This nut is located on the forward left side of the throttle bodies.)
Below are a few pictures that will help explain the procedure. These pictures are from a 1000 with special thanks to KLRman.
More reading on Secondary Adjustments can be found here.