I'm up past 45000 words on the re-write, and things are getting interesting. I'm convinced that I made the right choice in changing things, since it makes for a much more coherent plot (not to mention a decent parody) but I'm just hitting the stage where the changes are having an important impact on what is happening.
One of the most intriguing challenges is tying the main plot in with the most important subplot, which is essential both for reinforcing the ideas at the heart of the thing and for connecting it to the series as a whole. The trick is to do it in a way that doesn't seem too forced, and to make sure that the sub-plot plays a useful role in the resolution of the main plot. Possibly that still needs tweaking, just so that it doesn't seem like parts of two stories mashed randomly together.