I know it's difficult to diagnose the plant deficiencies but looking at some leaves, it did feel like the lack of PO4 so I will definitely check that out.Java ferns come from karst run off so need a good hardness to grow best. They like high flow and higher levels of po4 in my experience.
In regards to diatoms, have you used h2o2 in the tank? Also have you checked that the wood isn’t soft? I’ve had persistent diatoms before and the wood id used was mushy, once removed the diatoms went away.
Plant density helps, if I were in your position I’d throw in a load of stems floating for a few weeks to get things a touch more stable.
And the wood isn't soft but I am sure it's leeching all sorts of funky stuff in the scape. Unfortunately, I can't get it out now but from now on, I am strictly sticking with Riverwood.