I'm so sorry for your loss, it's just so much worse when they're just a baby.
It sounds like you have a competent vet, which is amazing, I've had two Dobes die of undiagnosed congestive heart failure. The second one, I caught-on to the symptoms and diagnosed him while the vet (an associate in the practice who was not my usual vet) was chasing what he thought was a mysterious infection that produced no elevated body temperature, no positive cultures, and no response to any antibiotics, even with the more unusual tests and drugs. I'm not happy about the wasted time, money, and trips to the vet on a wild goose chase of a misdiagnosis.
Anyway, there is nothing you could have realistically done if such a young pup was suffering from CHF. I'm guessing the vet did some differential diagnoses to go with deciding it was probably CHF rather than poisoning. I would've leaned towards poisoning from the medical history/onset of symptoms you provided, but only because she was so young. I'm guessing they did liver/kidney/blood screening, and found no evidence of acute toxicity.
The symptoms fit CHF. There will usually be elevated breathing rate, sometimes labored, sometimes coughing due to fluid accumulation backed-up into the lungs. There will be poor perfusion of oxygen to the body. There will be lethargy due to the poor perfusion. Seems to be a good diagnosis from what you describe, just really tragic.