The "staining" of your roots is most likely nute stain. You can add a tsp or 2 of h2o2 and they will go back to their pretty white color.

As for your rez change, I cant see the whole system in 1 big pic so I'm guess that you are extremly limited on space. This is what I do in my Cab. Go to either lowes or home dePOT and pick up a drill pump and you will also need a couple pieces of garden hose both with a female fitting on the end. Drill pump is in plumbing section by the sump pumps. Pump works on any drill. Pretty simple put the "in" end in your rez and the "out" end in an empty container and pump away. Do not run this thing for any length of time without water as it will burn up the rubber impeller inside so buy a spare while your there . If you happen to pass an auto parts store or Walmart on your way to get pump, stop in real quick and pick up a funnel used to fill transmissions (long skinny looking thing) that way you can fill rez back up without bending over.