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These are the kind of wrapped lines you typically get from a pdf conversion, and are probably in the original file. It is caused by each line being coded as its own paragraph.
Try converting to epub with heuristic processing turned on in the conversion options. This will probably fix a lot of it, but as the name implies, it guesses at where to unwrap. So it will almost certainly make some mistakes. Once you have the epub version, you can open it in the editor and fix the remainder using search and replace like gbm suggested. Then convert to a Kindle format.
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