I figured I would bump this a bit...
I have taken all my plants out of the tank, removed all the driftwood and fish. I totally stirred up all the substrate until the water looked like tea, as there was quite a bit of detritus and waste also.
I am starting over tonight. Now my debate is keep the silica, all cleaned and filtered, or switch to a Lowe's pea gravel. I have read that pea gravel is much easier to vacuum and maintain, but doesn't accommodate foreground plants well. I have Amazons swords, Crypts and Red Echinodorus which are all fairly low maintenance plants.
Would anyone talk me out of keeping the silica in favor of gravel??