If it does turn out to be the chimney or even the water heater issue. I
would just put in a power vent water heater and avoid the chimney
issue. I had chimney issues so I went with a power vent furnace and
water heater (Since they needed to be replaced anyway). I paid a little
more on the initial install over the cost of fixing the chimney but now
my energy bill is lower and i have newer units.
Next time i get the roof done I am removing my obsolete chimney.