Hey! I've been making kefir for a little while and what you're describing is normal. When I use Raw milk, my grains go NUTS! They Grow really well and usually end up fermenting my milk in less time! It
will separate with the grains on top with All the cream and lots of whey. I just shake it well...
VERY Well to try to get as much of the cream off the grains as I can, then strain it. Unfortunately, because of all the cream, it takes a while and you need to keep Tapping the strainer on the bowl, jar, container you're straining into. Just keep tapping until your grains are Almost all yellow. You'll Never get all the cream off and they'll still look pretty white, but I don't think it really matters.
I find if it gets to the point you're describing, it's also sorta fizzy and can be too sour for many. I really prefer my kefir when the small pockets of whey Just start to form. I'll drink it no matter how it comes out, but that's just how I prefer it! I've also found ways of flavoring it that always make it better no matter what

I don't always use Raw milk as it's not actually Legal in my state (Florida) for Human Consumption and is therefore about $14 per gallon! So, I use it periodically to give my grains a boost.