Hi, 

1. Shading Assignments Issue, 
          It because maya unable to find the shape name which is required for 
assignments of shader or its unable to break the connections from the previous 
assignments, to apply the new assignmrnts.
Going by your finding, extra ShapeDeformed mesh, you can while applying the 
shader assignments, check for the desired shape and apply the assignments.
Note: don't check for the desired shape by naming, check with couple of steps, 
a. which shape haivng the deformable history attached to it and b. it should 
not be an intermediate shape. 
In my previous studio, we had refrence shading pipeline, and where I am 
woriking currently has shaders embedded in rigs. Personaly, I like reference 
shading stuff because its increases the  modularity and brings flexibility.

3. Cache Introduction,
          There are commonly four stages in shot production Layout, Animation, 
Finaling and Lighting. You should introduce the cache system in your pipeline 
for the lighting department, that way the assets will be lighter in lighting 
scene

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