carbonate hardness in goldfish tank?

[susanp]

I have 2 10-yr-old "feeder" goldfish in a 40 gallon breeder tank.  Over the last year, I've been struggling with the water chemistry, and one of the fish was losing his scales and had a bout with fungus.  Now, both fish have fin and tail rot and pinhead-sized, raised white spots in a few areas on their fins.  I had been attempting to fix the water problems with more frequent (2x/week) water changes of 25%-30%.

Last week, a Petland staffer told me to test carbonate hardness, something I didn't know about. He said the  severe flooding our city experienced a year ago changed the water when wells were flooded, and that this is now a problem locally for fish tanks.   My tank water tested at zero.  I treated the tank with a buffer, added beneficial bacteria, and the good news is that the chemical balance is now perfect.  But now I have to deal with the sick fish.  (Petland had me put them on Pimafix and Melafix for now, but I can't tell if they're helping).

Yesterday my tank tested at Ph--7.2,  ammonia 0ppm,  nitrites 0ppm,  nitrates 20 ppm,  carbonate hardness 143.2.  I have 3 whisper filters running in the tank and treat the water with Seachem Prime.

1.  Will I kill off the beneficial bacteria and crash the tank again if I treat them with stronger medicine?
2.  What meds are best for the problems I describe?
3.  Why does my tap water test around 18 ppm for carbonate hardness, while the tank water tested zero?
4.  What else can I do?