Is there a way to create a different set of shield outlines on the map for Kings, Dukes and Counts that are pagan? Most of the pagans have shield outlines similar to Christians, and some have similar to Muslims. Is there a way to make my own shields for different pagan religions that would show up on the map?
To create different shields, you would need a 3D Modeling program like Zbrush, Blender, or 3DS Max. You would need an image editing software like Photoshop, Paint.net, or The Gimp to make the diffuse, specular, and normal maps on the unwrapped UVW templates for the shields. That whole part is pretty easy if you've any experience in 3D modeling.
Unfortunately, 3D Modeling programs are expensive (3DS Max, for instance, is regularly thousands of dollars). Also, the files are encoded in .xac from Emotion FX, and the license to use that plugin is somewhere around $10-15k. I've seen some forum posts for other games where they've successfully made .xml converters to change the spline data and convert .xac files to another format like .max, but I'm not certain where they are.
Additionally, even if you crossed the immense financial and/or technical hurdles in creating a useable shield, I've found no reference in any line of the files that delineates who gets to use what shield and why. I suspect it may be hardcoded.
tl;dr - I don't think so.
Wait, which pagans exactly have similar to muslims?
At a casual glance, the ruler of Perm in the 1066 starting scenario is pagan and has a muslim shield. I suspect that's because his liege is Sunni muslim. (Vassals may inherit the shield type of their liege?)