I wish I could help, but I'm just a newcomer. However, am I correct in understanding you are only feeding the plants with what the Danios provide naturally? We've been adding some liquid plant food to our new tank, since it is new. Don't know if eventually we can stop that as we get more fish added and provide a better biomas for the plants to feed off of.

Also the small circular nature of these yellow spots makes me wonder if that is really a nutrition problem. Hope someone else is able to nail this down for you.