I do not think bad bacteria is your problem.  First thing I will note is that guppies like salt almost all fish, even fresh water fish like some salt.  It maintain osmotic pressure will helps them to absorb nutrients from the water and their food. I add about 1 tablespoon of Aquarium Salt per 5 gallons of water.  Salt does not get comsumed and does not evaporate, so when changin water only add salt for the water removed.  The box should have instructions. Salt will encourage the guppies to breed, not that guppies need much encouragement.

Last but most important is your test results. A KH of 0 is bad.  KH does 2 things.  First is stablizes pH, if KH is 0 nothing is stabilizing the pH and it could change drastically with in even 30 minute time frames.  Even if it stays in a healthy range the constantly changing pH is bad for the fish.  Second KH with pH tells you the amount of CO2 in the aquarium.  A KH of 0 always means there is no CO2.  You should maintain a CO2 of 10mg/l to 20mg/l.  At a ph of 6.8 that is a KH of 2 to 4.25.  At a ph of 7.0 you need a KH of 3.25 to 6.5.  In general higher pH means you need a high KH to maintain the same CO2 level. 5mg/l is the minimum amount of C02 for photosynthesis, while 30mg/l will cause resipritory problems for the fish.  KH boosters are often solid as pH stabilizers.

If you do tear it down and clean it out, consider a fish-less cycling. Angelhologram has a  great article on that in Immediate Help. I need to memorize it!

That might give them a better start. Empty tanks don't really cycle because there is no ammonia/ waste material (excepting some plant material) to get it started. I applaud your careful approach though.

The symptoms do sound a little like bacterial problems. When we add a bactericide or antibiotic, we also tend to kill the beneficial bacteria and take the tanks back to step one in the cycling process.

Another thing to watch out for - an all of us have probably threatened our fish - inadvertently - this way. We use household cleaning agents (including ammonia and chlorine) or spray bug sprays or even (at least here) have things like Shell Pest Strips to zap insects. The list of potential poisons is long, maybe (I remain skeptical of this) even cigarettes could be included. Formaldehyde in the insulation of older houses here has also been questioned.

I scrub down with baking soda to get as much soap residual as possible off before getting into the tanks. Probably could do more water changes instead. ;)

After your careful start, you have got to feel like "no good deed must go unpunished." I would certain at least rinse out the tank and gravel and filter very thoroughly. (Actually I would bleach the tank and filter and boil the gravel - but that is because I need to get a life.) I wouldn't do the fish-less cycle because I can import the gravel, plants, and water and if I plan ahead, filter from other tanks. If you have a nearby aquarist friend with a healthy aquarium that is a possibility. (Tell him or her that this crazy American suggested it.)

If not importing the cycle, I would try the fish-less cycle. And maybe a couple of days before putting the fish in there, get a few again, just like you did, and put them in a clean, soap-less container. I would give them a treatment for internal parasites. Without those, the fish's immune systems can more effectively deal with the bacterial threats. It is also neat how the anti-parasite treatments sometimes take out other nasty wee beasties too.

Was the rock from an aquarium shop? Even they still make mistakes sometimes. What was the rock?

When getting plants, you might want to cleanse them too. I offered a few suggestions in the IH area.

A real long shot, but if you use frozen food, make sure on the one hand that they are well rinsed in Luke warm water after defrosting and also make sure that nothing has spoiled, if extra was kept in the refrigerator.

Just kind of throwing things against the wall to see if anything sticks. ;)