I like this idea a lot, GreenPilgrim. The 'floating island' concept has always been a bit of a favourite of mine.
First, you might find it interesting to know that the mountains in Avatar were based on the Zhangjiajie Mountains in China. The Studio Ghibli film, 'Laputa, Castle in the Sky', might also give you some inspiration.
The major problem I see with your layers image, is that none of the islands overlap each other. You would expect that as the floating islands move around, some would pass under or over one another. I can understand why you would not want to do that, as it obscures parts of the island that are beneath a higher one, but I think your sketch wouldn't look right unless you added some level of overlap of the islands.
Fortunately, I have an idea of how you could do it, which wouldn't necessarily involve more work (but might not be consistent with your 'vision' of this map--ultimately, it is your decision). My idea is to have the central part of your map showing the islands as if viewed from above (with overlapping areas, as described above). However, you could include somewhere else on the map each island mapped separately in its own inset. The diagram below shows what I mean.
I really like the idea of having the overland map below, and using a cloud layer.
To depict islands of relative height, perhaps you could simply use thinner lines and more saturated colours. Some of the lower islands being overlapped with clouds might also help.
Hmm, perhaps I got a bit carried away. I'm keen to see what you do, though.