First thing, WELCOME!!
As far as rebuilding the slave cylinder, the best thing to do is replace, not rebuild. Although you can rebuild, many many of us have found out that the rebuild sometimes does not last long, or does not work out as good as it should, all depending on the condition of the cylinder, and just how much you have to hone the cylinder walls. A new replacement slave is only around $50, give or take. A rebuilt slave is a rebuilt slave, not as good as new, and the next thing you know, it needs replacing again!!
Not being where you are, it's kind of hard to guess what is wrong with the rebuild. Although the Barnett setup is a good one, there is an easier and less expensive fix that many times does not require a complete teardown of the clutch. It is a replacement heavy duty "disc" spring that looks like the stock one and is made by PCW racing. Of course what you did is going to give you a nice strong long lasting setup! Now, did you replace the clutch plate with the heavy duty version made by Yamaha?? If you did, then you did not use the wire that was with the stock one?
If you look it the tech read only section, there is a great step by step illustrated set of instructions on how to rebuild the clutch...
http://www.venturerider.org/forum/showthread.php?10518-Clutch-Upgrade
Hopefully this will get you started. If the hydraulic clutch worked fine before you did the clutch, I would suspect it still should be good, or as good as one with 50K on it can be. I suppose you possibly could have blown the internal seals but part of me doubts it. It's just a simple piston arrangement, nothing special about it...