I decided to swap out the stones. Going to boil and bleach them. Tomorrow I'll put the old stones back in. The new ones seem kinda crappy.
I'm still getting this brown gunk, still unsure if its bacteria or algae. I did a water change on the 23, that was a day shy of 3 weeks from start. I didn't see any build up during that change but I wasn't looking for it either. The water change was done rather hastily as I was trying to leave for Thanksgiving. I also just topped off with plain ro water, I would say 2.5 to 3 gallons.