im still a little confused about this as well Tiny...

Your brown roots sound like mine... I thought it was from the bat guano FF stuff... Big Bloom. My roots are totally brown and eww looking. Have been for awhile but absolutely no negative effects on my plant. In fact its the best looking plant ive ever had. I also use tap water.

I have my water lvl super low compared to the bottom of the basket... Maybe 8-10" and mine does fine. Id love to hear the proper lvl from some more experienced people.