I've had this 9 gallon fish tank for a couple months now. At first, I bought one Betta, but a couple days later I bought three Corydoras. Only a couple weeks later, my biggest Cory died of popeye. I tried treating him, but I didn't get the medicine in time. The sinking food I had bought for my Corys was the cause of the problem because after a couple hours it turns into big balls of mush and the bottom was pretty covered in it. After he died, I kept some of the water from the tank and cleaned the entire tank, rocks and all. It ended up being about a 75% water change. For a couple weeks the rest of my fish have been fine, I've been sucking up the food gunk from the bottom weekly and doing everything I'm supposed to (such as add Cycle weekly and Waste Control) but now the tank is twice as dirty as it was before, and another of my Corys is dying of something unknown! The rocks are turning brown (what the hell?) and so are the leaves of the fake plant and the one real plant I have.

What am I doing wrong and how can I fix this? Please help!
http://tinypic.com/r/b5mk29/3
http://tinypic.com/r/210yu1e/3
http://tinypic.com/r/16knry0/3
http://tinypic.com/r/2gtnh3c/3
http://tinypic.com/r/2ew0ev7/3
(Sorry the pictures are a little fuzzy)