Just curious.......what are you feeding them? How much? How often? When? I ask this bc you mentioned that the water smells. Do you remove uneaten foods? Not trying to insult you, but to explore all avenues
Imo, your fish are very likely to be just like all of ours. Your fish are putting into the water the same products ours do and it’s not a problem specific to your fish like they have weird slime, dirt on them, but to the water. I might suggest you do remove the root and thus eliminate one more potential factor. Go bare bottom so you can see all possible uneaten foods and thus eliminate foods getting stuck in gravel or sand. Your bacteria always need surface area to attach to. Running an empty canister is not helpful as I see it. As suggested, have someone hold your fish for you while you get that water cycled/established.