The second stage of the process is to create a shaded relief, so I could drop the original colors of the elevation map. The original file was enlarged 300% and then I went through a number of trials until I found nice "bevel and emboss" parameters for the relief. I found the right parameters depend on the scale of the original elevation layers. In this map, bevel was at 10%, 3 pixels wide, colors for shadow depending on heightlevel), but as I said, it is a matter of trial and error.

Once this was done, I had the land mass colored in a solid neutral color and traced the main rivers (which were drafted already in the original file, by the way).

The file is large, so I am posting only a reduced and cropped image of the result.
Click image for larger version. 

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The shaded relief is really beautiful in my humble opinion, and I felt pretty excited with it, but it was very "bland" at this point. One of the things I would love to do, since I am working on climates at the same time, is to use Natural Coloring on top of this. But having a mouse to paint and not being an art-trained person, this was just too difficult for me and I ended up giving up on it.