We can take a step by step approach at this one.
Your tank established an equilibrium with the levels of light, nutrient and CO2. The indian fern is a terribly fast grower, and sucks up a lot of nutrient. Taking that plant out caused an imbalance between the amount of nutrient that is available for the plants to absorb vs. the amount of light, and all of this is relative to the new CO2 levels.
Add an excess of ferts (comprehensive or similar) and that should help some things.
Can you take a closer up pic of the filamentous algae? I have a hunch at what it is, and I hope that's not it, but at this point the fibrous stuff could well be the roots.
The brown stuff on the Java fern is how the plant reproduces underwater.
Add JBL balls under the roots of the root feeders like sword plants, and some ferts in the water (too much is more expensive, but better than too little).
The same rules apply to most tanks.
Thank you for the informative and well thought out post.
You can also test the water for Nitrogen and Phosphorous (Nitrate and Phosphate).