Hello Kerbouchard,
I'm nit really sure what to make of the brownish roots at this point. It could be nothing, or the beginning of something. The
nutrients themselves have a tendency to tint/color the older roots. Though I'm not sure what organic smells like, so I'm a little confused there. But if the roots don't feel slimy, and the foliage is nice and healthy, I would be leaning toward nothing to worry about yet. From the pics they all looks real good to eat. Even that Oak Leaf one looks like it has a nice deep red color to it.
As for rotating crop, I would build a small water culture system for the seedlings until they get big enough to put in the main system (pictures attached). Using just a short flat storage tote with a lid, an air
pump, and air stones work nicely. Use the same baskets you use for the main system, so you don't hurt the roots when you transplant. But place them as close as you can in the water culture system to make use of as much space as you can. It wont matter that they are so close, you'll be transplanting them before plant size becomes a problem.