Flushing

You need to give us some more information, how much water did you use? You should flush ur soil with 10x the amount of water the pot can hold. I think it will never be very clear.

depends a bit.. usually i get mostly clear runoff after first few irrigaitons as any loose pith flows out with water, but eventually that is very minimal over time. as long as your roots aren't slimy or stinky, probably not gowing anything on them... staining can occur from normal fertilizer too.. the slimy part helps discern. if not hydro, can inspect after harvest to confirm. the water typicalyl won't be drastically different, but products used and other non-problematic causes are possible.

It's running through soil, right? Does a mud puddle have clear water before it settles down? No, you're fine!