Can you try to use several independent plots instead of using subplots? That will make it easier to include the plots one after the other in the narrative doc while allowing for interweaving text comments and explanations in between.

Here is another example that uses multiple plots at once: 

https://github.com/scikit-learn/scikit-learn/blob/master/examples/manifold/plot_compare_methods.py

and here is the narrative doc that re-uses the plots:

http://scikit-learn.org/dev/modules/manifold.html#introduction