Ok, this one is getting to be a real pita! Have been at it for 3 weeks.
Started getting occasional running of commode a month ago, presumably
due to leaky flapper. Replaced flapper, still running, so replaced both
fill and flush valves. For fill, went with Fluidmaster plastic; for
flush a Douglas brass valve. I decided at the time to try using the
ball and rods for flush valve seal instead of flapper. In one case, I
was able to get a fairly good seal, but the darned rod would want to
stick sometimes after flushing and wouldn't seal the valve. Tried
readjusting alignment of rod, but still would occasionally stick. So,
getting fed up yesterday, I decided to go with a Korky flapper of the
kind that slides down over the brass overflow tube.

Despite all efforts, which has included so far, continual adjusting and
readjusting of ball alignment, a "reseating" kit for the flush valve,
and now switching to a Korky flapper, I am still seeing about 1/2 inch
of water loss over an 8 hour period. This isn't enough to trigger the
fill valve, but if I went away for a day it certainly would be.

I'd appreciate any ideas at this point. I'm about pulling my hair out
on this one. The best seal I seemed to have was with the ball seal but
I couldn't get the rod to stop sticking going down sometimes. I even
added more weight to the rod and readjusted the rod guide, but to no
avail. I would have thought going back to the traditional flapper would
have solved all of this, but it hasn't.

Any ideas would be welcome. I never thought I'd have this much trouble
getting a proper seal at the flush valve seat!

Bill