A lttle advice before you get started. My advice comes from the "been there, done that" category on front brake master cylinders...
Take the whole master cyl assembly off the bike and take it apart. Carefully inspect the bore of the Master cyl for "pitting". If you find pitting the master cyl is TOAST! At that point, I would keep an eye on ebay for a used one in excellent condition. You will pay far less than a new one in that case and guys are taking them off wrecked bikes all the time. If you can't wait, you will have to buy a new one.
If you find no pitting, do what Paul said and buy you a piston cup set from ron Ayers.
Pitting is causeed by water in your fluid causing corosion in the master cyl. It especially occurs on bike that sit outside and do not get thier fluid changed regular. The darkening of the fluid almost always occurs on the clutch side first (before the brake). I'm not sure why this is but, I think its because the clutch is used more oftem (every time you shift).
Good luck....
You will need a snap ring pliers to get this job done. Do yourself a favor and buy one before you start. They can be had at Sears.
Dave