Maybe your grains have become contaminated. I've never used the grains before, only the powder but I've heard that sometimes after they are used many times the ratio of bacteria to yeast can get out of whack and you don't really have kefir anymore; not anything poisonous but not technically kefir. It's up to you if you want to keep using it; trust your nose and other senses.
As for the whey, I've never been able to get mine completely clear. It always has a little swirl which I think is harmless. Maybe someone else can input on this?