Mistakes made, but I thought I was finally doing everything right

I did a water change yesterday, about 60%, and today, 24 hours later, I've got a young zebra danio (who was born in the tank) swimming weakly. He looked energetic this morning. This is so frustrating!
 
It is about an inch and a half. I'm wondering if I should take the whole tank apart and replace the sand with some kind of gravel. The zebra danio died last night.
 
Just to clarify, this is a 5 gallon tank? Sand substrate with live plants?

What fish, and how many? Do you know what plants you have? And are you dosing fertilizer?

How much Prime do you use? (Asking because it has a pretty strong odor in the bottle.)
 
Yes, this is a 5-gallon tank with fine black sand substrate and live plants.

I now have 3 celestial pearl danios, 1 otocinclus, 1 Malaysian trumpet snail.

I do not use fertilizer. My plants have gone crazy without it. I have one betta bulb, 1 large "bunch" of java fern (I'm pretty sure), and this other plant in the photo, which came in a little pack of gel from Petco. It started out as about a dozen tiny (half-inch) blades of "grass" that has now grown into this lush plant that is probably 8 inches tall now. If you know what it is, please tell me.

I now add 2 drops of Prime (from a medicine dropper) for every gallon of water I add back into the tank. I use a bucket that I got from Lowes that has a 4-quart mark on it so it is pretty accurate.

IMG_0866.jpg
 
Just did a 25% water change. I stirred up the substrate around the plants pretty good and did not smell that rotten egg smell this time. I did really turn up the sand several days ago when I did the bigger water change.
 
Is the java fern planted in the sand? Am asking because java fern will rot if the rhizome is buried, and rotting plants can smell like rotten eggs. (Same for bulbs that rot instead of growing - if it feels squishy, it's dead.)
 
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