I used those alphas to mask-select polygons on basic primitive 3D shapes such as cubes and cylinders. Then I deformed the polygons that were not masked. Here are some examples of the 3D tools I came up with by masking and deforming:
I did not use any texture for those. Their texture is just a tweaked material shader created by Jantim at ZbrushCentral.
After I had my library of objects, I placed them over my under painting, using the canvas Gyro tool, to push them back or pull them forward.
Here is my image with all of the 3D tools placed. Apart from lighting them with 3D lights, I also used the Intensity and the Highlighter brush to establish light and shadows.