Rust/black color substate

[proff1949]

About a month ago I posted pics of a red fluffy substance growing in my 55 gal FO tank. The substrate also had a rust colored growth on top of it. I was informed that it was Cyanobacteria caused by excessive nutrients and poor water flow in the water column. Suggested remedy was major water changes and improved circulation all of which have been accomplished with a through cleaning, weekly water changes and the addition of an additional circulation pump.
However today the rust color is still actively accumulating on the bottom along with black/gray streaks IN the gravel base.
Im about at wits end with tank. Its just over four years old and has been plagued with water quality problems since its second year.
Sure could use some additional insight before I pull out the rest of my hair.

 

[Sniperhank]

Sounds like the issue stems from the gravel bottom. The stuff traps nutrients and can restrict flow in the gaps between individual gravel pieces.
I'd remove the gravel bottom and replace it with a sand one. You'd be able to do this with a long piece of box pipe to avoid a sandstorm in the water column.
It'd need removed over added on top due to the sand grains will fall between the larger gravel pieces over time leaving you with a gravel bed again.

 

[proff1949]

sand bottom

That was my thoughts earlier this summer when the problem really became apparent. Since then the entire bottom has been changed to sand. This stopped it for several months but now it is back. I wonder if its a problem with debris trapped in the sand itself? I agitated the surface this morning but you can almost watch the bottom change color. About ready to go back to raising guppies...

 

[Sniperhank]

If that is a sandbed only months old, no way is enough trap this issue.
How often do you feed? What do you feed? How much do you feed?