Well for starters you'd be better off controlling your fake stones distribution by having them as children of a surface layer. This way you can specify exactly where you want them and control their colour. You seem to have many surface layers and stone layers that are overlaying each other to an extent that its hard to know what should show up where, and without the terrain you've used it's impossible to say. Try giving your stones bright temporary colours at first to help locate them and check their size etc. then when your happy adjust the colours to suit your scene.
Remember also that the order that you place your shaders greatly affects the final look, layers at the bottom of the list being at the top of the terrain. All I can get from your file are green displacement spikes.