I cheated. I didn't grade papers this afternoon. I made a copy of the fugue and attacked it with colored pencils. Subjects were colored blue, counter-subjects green. Episodes were highlighted in red. Tacets are yellow.
The red episodes always begin when the combined blue and green subjects and counter-subjects come to an end. The yellow (tacet) sections sound thinner and restful before the notes plow into greater intricacies.
Coloring it all makes it make so much more sense to me. By the time I finish the analysis, there will be very little of the white page left. It'll be a while before I get to that point, though.
All and all, it was a very satisfying experience. Now I'm finally grading papers and writing quizzes.