I'm coming to this one a bit late, but my guess is the reservoir o-ring is leaking, and it might just be some corrosion where it seats.
If the brakes work fine, a rebuild isn't necessary and I wouldn't touch the rest of the master cylinder. Well, they're so easy to get into, I tend to take a look and clean up what ever I find, then put it all back together. Save the rebuild kit for when it's needed.
As for honing the master... don't! At least not with stones! The aluminum is too soft and too much will be removed. The best method uses a wooden dowel with some wet/dry sand paper, and twirl low speed. check often. Doesn't take long.