Seangee posted as I am typing, and I agree this is not likely the issue. Guppies in water with a GH as high as 300 are not going to have trouble leading to death for that reason, even if the pH is 6.8. But these numbers for GH (300 ppm) and pH 6.8 do not make sense. And by "Alkalinity" are you referring to the KH (carbonate hardness)?
We still need to start with your source (tap) water. You might find data on the website of your municipal water authority. And are you doing anything with the water, such as additives, substrate material...anything? Please list all additives.
I am not following the cycling...if the filter media dried out the bacteria would all have died. Did you keep it wet for the two days?
Nitrate at 40 ppm is high, but this also would not kill guppies so rapidly, though it will weaken most fish. Have you tested the tap water for nitrates? Nitrates in the source water is one issue, and nitrates occurring from within the aquarium system is another.