In my previous test, I was working with with a fairly simple setup in which I had one character, one texture and no background. I found the method I used was successful, but the next challenge was to account for scenes with multiple objects which each have a separate texture.
As I set up the render, I decided to use a variety of passes to aid in compositing overlays of textures, which I create in photoshop, and achieve the desired effect, breaking them down as follows:
1. Albedo Pass
This pass is what I consider basic beauty pass for the film. All the objects are shaded simply with a surface shader of their base color. The shaders also include any "non-static" texture patterns, such as the freckles on the character. I have decided to separate shadows and highlights from this pass, unlike a standard "beauty pass", since separating these elements into their own passes will give me greater flexibility in how I decide use them in the final composite.
4. Sub ID Mask Pass
Similar to the Character ID mask, I further assigned surface shaders to specific objects (the character's clothes) which I want to fully mask out. Having these masks solves my specific problem of allowing different patterns to show through wherever the characters clothes are in the shot.
With all the different passes rendered, I began the composite in After Effects.