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If the OP is still following this, the app I linked to in my previous post is basically a tool to apply various preconfigured regex in series. It then displays the results. If you like it, continue to apply various regex, etc, until satisfied, then export the result to any file you like, including the original.
It's got some patterns that search for the things being discussed in the thread.
One of the things that you can search for, and may not be obvious to someone just looking at the text, is a space preceding a hard-return as a marker for end-of-paragraph. I'm surprised how frequently that has turned up.
Luck,
m a r
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