I'll chime in here about the spots on the Java Fern. I am nowhere near an expert here, but maybe my experience can help you? I went through exactly the same battle as you. Then, I moved my Java Fern to a completely different tank with NO lighting (except for the sun that comes indirectly). Java fern was thriving. I have come to think it is super sensitive to too much light?
I notice you've got well water like me, if I'm not mistaken? My well water has a ton of minerals, and is typically very hard. I also have super high phosphates from the tap too, and I use special filter media to remove some of them. Because the tap water has so many nutrients already, I don't really dose the water column except for the occasional Excel or Flourish as needed.
The two changes that cleared up algae for me were reducing the lighting (I reduced intensity, not duration), and adding Fluval Clearmax to the filter have made the biggest difference. And time. I made those two changes and waited. Like, a month or two. New Java leaves are spotless, and much less algae (it's still there, but getting better).