Speed bumps in the text

I usually edit each chapter with Autocrit as I finish it, but this has been a distracting year and I've missed a lot of them, so am currently putting the whole of Unofficial Girl through the Autocrit software. It's rather wearing, doing it all at once.
The main thing I need Autocrit for is my word echo problem; you'd think that as I'm aware of it I'd be able to deal with it, but I still miss some of the most obvious instances. It's brilliant for that. The other areas it focuses on are less useful, and some are counter-productive. For instance, on one occasion I used 36 adverbs instead of the 35 allowed, so EVERY adverb was in red - distracting. And the software has recently changed, and become a lot pickier. I preferred its more laissez-faire version.
At this stage, I'm eliminating speed bumps in the text; anything that will trip a reader and remind him that he is reading a book. I'll be reading it aloud next. The aim is to make the prose as smooth as possible. This is something readers like, even if it's not consciously appreciated. Indeed, on YouWriteOn and Authonomy, I suspected there were those who marked down an easy read as somehow inferior to more taxing writing. They were deeply wrong.