The comma stuff can't be gauged by a computer. In english there's an abnormal amount of leeway between punctuation marks and you can imply a lot by lengthening or splitting sentences. It's also one of the few ways to make a paragraph flow in a satisfying way without changing the words, because of the way people read stuff in their heads. I often find myself obsessing over commas and semicolons because of how important they are to the meaning/rhythm/structure of a text.
Picked a nugget of text semi-randomly:
Of course she had never been to Berlin, or any other major city, during the those days but from time to time, she still caught their parades and celebrations on the old black and white TV they had back home, before it broke.
"Of course she had never been to berlin" and "Of course, she had never been to Berlin." Have slightly different meanings because of how you'd say them. With the first sentence I'm inclined to put stress on 'course', and I'm accusing the reader, or a third party in the book, for not knowing that. In print, I'd put that in italics.
The second sentence is probably what you were going for here. It sounds a bit more impartial in its 'of course' because of how the reader is forced into a certain speaking pattern.
A computer would've ignored this.
You've also got:
...Berlin, or any other major city, during the those days * but from time to time, she still caught their parades and celebrations on the old black and white TV they had back home, before it broke.
The space marked by the first asterisk is crying out for a full stop. Parts of the sentence afterwards actually flow pretty well and are nice to read, even in my head (parAdes and celebrAtions), but to read the entire thing as a single sentence kills that.
The slightly strange clause order is also to blame. The 'before it broke' at the end is abrupt and ends the sentence in an unsatisfying whimper. Replacing "from time to time" with "before it [finally died]" seems better to me. but it's your story. You should be able to recite your writing in your head the way you want it to be read, and adjust accordingly.
Sorry for being so anal but it's bothering when popular writers don't bother making their work satisfying to read. Making a paragraph of exposition sound like water trickling along a fresh alpine brook will give readers a reason to trudge through five hours of inaction in a book.
The ninjas are in full force today.