Plenty of info in the prior posts about this, too. Guys were doing the fix long-before I wrote this up (below).
http://www.vmaxforum.net/showthread.php?t=21799&highlight=Master+cylinder
I added some content to the excellent initial troubleshooting "firefly' presented. I also added some content at the end about the brake system since they both use similar components. Because of my 'baby-boomer' eyes, I also had to make the font high-contrast to make it easier to read. I can't easily read the 'stealth colors' (low-contrast).
Symptoms of clutch master cylinder or slave cylinder failure, an internally-collapsed rubber hydraulic line, or low fluid may include:
1- Difficulty in finding neutral.
2- Difficulty in shifting up and down.
3- A 'dragging' clutch.
4- Fluid loss or leaking may or may not be present. Places to check for fluid loss include any and all connections and components. For example, when the seals begin leaking in the clutch master cylinder, you may notice 'wetness' on the clutch lever as the fluid bypasses the seals and runs-down the clutch lever to the ball on the end. Using a white paper towel to dry the lever and then repeatedly operating the lever will cause the leakage to collect again on the lever and is usually first-evident at the pivot point area. if left alone after repeatedly operating the clutch lever, the fluid will again run-along the length of the master cylinder lever, and be present when wiping the entire lever surface with a new white paper towel.
5- Bleeding the clutch slave cylinder fitting temporarily relieves the symptoms but they return.
6- As a result of a faulty or failing clutch master cylinder or slave cylinder, missed shifts may occur because of being unable to fully-disengage the clutch. When you operate the clutch lever, instead of easily being able to select another gear, you cannot easily 'find' the next gear going either up or down.
Note: the metal pipe that connects to the master can easily bend or even break when tightening the banjo bolt. Pay attention while tightening the bolt. Hold the assembly so that it does not rotate, bend or break.
7- Leakage can occur at any point of the system, and includes all connections.
8- Annual flushing of the brake/clutch system w/fresh fluid will remove contanination and water from the brake or clutch system, reducing internal corrosion and leakage possibilities.
9- An internally-collapsed rubber hose may act like a 'one-way' valve, passing fluid but not allowing it to return.
The same symptom can occur when the master cylinder small-diameter hole (there qqare two holes visible in the 'floor' of the master cylinder reservoir, one larger than the other) becomes plugged with debris. A way to check for proper operation (careful with this, because brake fluid can easily leak out of the open reservior) of the hole is to remove the reservoir cap and to operate the clutch lever. It is easiest to do this with the bike on its centerstand or while using a track lift to hold the bike upright and the bars not to full-lock, but in a 'straight-ahead' position. When you look inside the reservoir, there should be a discharge of fluid from the small hole on the floor of the reservoir, evident as a tiny 'fountain' of brake fluid which discharges straight-up as you squeeze and release the lever. If you do not see the 'fountain' of fluid, then your hole is plugged. You can try to remove the fluid in the reservoir and use a tiny needle or pin or drill bit to dislodge the contaminant, but since you are going to be having to remove the piston/seal shaft and replacing the seal shaft with a rebuild kit, that is the time to thoroughly clean the entire reservoir, including that tiny hole.
Note: when disassembling the internal snap ring behind the clutch lever pivot holding the piston/seal shaft, it is not necessary to use a pair of snap-ring pliers to remove the snap ring. Because of the tight dimensions inside the cast body of the reservoir past the pivot point of the clutch lever, if you use snap ring pliers, you need a pair with very long 'noses' on them. You can usually substitute a mechanic's straight 'pick,' which is nothing more than a straight awl. Place the point of the awl into one of the snap ring holes and simultaneously drag it towards the other end of the snap ring, the one that has another hole, while you carefully lift up with the awl. What you are trying to do is to unseat the end of the snap ring from the ring 'land' or groove in-which the snap ring is seated. Once you get that end of the snap ring unseated, you can either try the same thing with the other end of the snap ring still in the ring 'land' or groove, or you can use another mechanic's pick which has a 90 degree bend in it to pull out the unseated ring as you work towards the seated end. This is how I have rebuilt a number of my own master cylinders, it is easier and faster than trying to simultaneously engage the tips of the snap ring pliers into two holes you can barely see. And, please don't try to do this with the master culinder still on the bike, it is much easier with the master cylinder off the bike and disconnected from the banjo hose fitting! When you are ready to reinsert the snap ring, you can either use a small screwdriver to get the snap ring back into its groove, or use a small 1/4" deep socket that is slightly smaller than the interior diameter of the master cylinder body. Normally you can feel it 'click' into place as the snap ring seats into the groove.
Replace the brake fluid with fresh fluid, use a Mity-Vac or a 'speed-bleeder' to bleed the system, and test full release capability of the clutch and all connections for any leaks before returning your bike to service on the road. Don't forget to clean-up all spilled brake fluid to preserve painted parts!
A leaking clutch slave cylinder will usually reveal itself due to deposits of brake fluid under the bike on the left side in the vicinity of the slave cylinder and the engine side cover, or on the ground. Brake fluid is clear when clean and has less viscosity ('thickness') than motor oil, which usually is much darker in color due to contaminants in the oil.
The same procedure can be used to deal with similar problems from the brake system's master cylinder. If you see brake fluid on the calipers from a leak, and find the pads are contaminated, you need to replace the pads and disassemble/clean the calipers. Most mechanics would replace the pads in both calipers at the same time to be sure of having the same friction compound and wear from that point. It is often not necessary to replace the caliper seals if you are careful in disassembly and cleaning, you can re-use them if they are in good shape. Do not forget to use a bit of brake fluid to lubricate the square rubber piston o-rings before re-inserting them, and use a bit of brake fluid on the cleaned piston surface where the o-rings contact them. Properly-cleaned and installed pistons should easily be able to be moved in and out with finger pressure inside the piston depression before re-installing the calipers on the fork leg or the rear wheel carrier while they are 'dry' before filling them with fluid. The best tool for cleaning calipers I have found is a Dremel tool or similar rotary tool, while using a variety of brass bristle brushes. I use a brass bristle disc and a cup brush, (and a 'flapper' wheel, maybe 120 grade, for the piston exterior) to thoroughly clean the o-ring groove. The flapper wheel is also good if the caliper body is experiencing a build-up of corrosion.
Following these steps should cure most of your issues with your hydraulic systems.
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