There are 6 total. 1 in the Flame Peaks, 3 in the Verdure Forest and 2 in the Moorsh Grotto (1 upper, 1 lower).
I've been scouring that Grotto for hours and I cannot find the second one. Does it get locked out after the cave gets change around?
No, it doesn't. One is down in the same area where you find the first runestone, and the other is up above in the main area. You have to climb to the top and drop off a certain ledge (one that has a nice sparkle near it) to find it.
