The Ghost Palette is a palette that tells Populous which color it should use from the Main Palette when it want to mix a color with another. It mostly used on the User Interface and in Software Render after worshipping something, it generates the dark effect by this, also all transparent effects (like the Encyclopedia is rendered to the game screen using this).
The image size is 256×256. Each row and column represents the color on the palette. Pixel number x,x is the color itself as it is used when it won’t mix anything (such pixel 1,1 is the first color on the Main Palette, 2,2 is the second, ect.). As you can see, all colors meets with all colors, so Populous can mix any colors with any. For example, when it want to mix color 13 with color 35, it uses the color located in row 13 column 35.
To make this palette use Photoshop. You need to open a new RGB color image (we will put the palette on it later) with 256×256 size. On the background layer draw lines to every column. The line color must be the color on the palette, if you drawing to the first line, it must be the first color, the second column the second color, ect. The line must fill the full column. After you done it, you will see your full palette on your screen in lines. Now duplicate the layer, put it to the top and rotate the newly created layer 90° Clockwise, you should see your palette rotated. Now set Opacity of the rotated layer to a value between 40-60% depending on the colors you used. If you used dark colors set it to a lower value, if you used light colors set it to higher. In most cases 50% is a good choice. Now set the image mode to Indexed Colors and load the palette to it. To do it, use either Khick’s Palette Converter to convert Pop Palette to Microsoft Palette or save a palette from an image you extracted with Ted’s Raw Editor then load it to the image (for example you can extract the bad Ghost palette to get your palette from it). Now save as a 256 color bmp and import it to the Raw Editor, and save your file.