I don't recall ever seeing the clutch fluid turning grey. I usually see it turning a reddish or a brownish color. A greyish color almost seems like water contamination. It could just be my limited experience in changing clutch fluid I suppose. One of the things that I don't like with the design on this bike is that the fluid stays trapped in the slave cylinder doesn't get flushed along with the rest of the fluid when you do the clutch bleeding procedure.
I would also suggest, like Mike did, looking at the shifting linkages as to a possible reason why you had problems shifting into third or higher. I seem to recall (perhaps incorrectly) some time ago, someone having a similar problem that was solved by lubricating the linkages.