1) approx. 2 monthsI have a few questions as to the timeline.
1) How long was the puffer in the tank before you added the other fish?
2) How did you cycle the tank?
3) I see you have your ammonia and nitrites listed in the first post, but what were the nitrate levels?
Just saying perfect, unfortunately, doesn't help much because one person's perfect is not the same as another's.
4 & 5) I also see you add cycle every week, what water conditioner do you use to remove chlorine and how much water are you changing when you change it?
I wouldn't jump to parasites, parasites don't cause the rapid breathing you indicated in the guppy. Ammonia, nitrite, nitrate and chlorine cause rapid breathing. Parasites cause the reverse and a fish that died of a parasitic infection will often look gutted and sluggish and have decreased ventilation rates and food intake before it dies. I don't know of any parasites that kill that quickly or without at least one of those symptoms. I think there are more things to address here, before you jump to treating for something, which may make the problem worse rather than better.
2) By making water changes and mostly using the Nutrafin aqua+ and cycle. Oh and I've waited until the water came out clean (tests all perfect).
3) my test is for nitrite and nitrates; therefore the nitrate is at 0 too.
4 & 5) I use Nutrafin aqua plus as water conditioner and I do a 20% water change.