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The \r\n issue was solved when I changed to a POST request.

But, since I was retagging questions (didn't really need to change the body, just resend it), I ended up using the body_markdown, encoded with HTMLParser.HTMLParser().unescape()

body_markdown = str(HTMLParser.HTMLParser().unescape(question_data['items'][0]['body_markdown']))

<%%>

And then sending it with:

response = requests.post('https://api.stackexchange.com/2.2/questions/'+str(q_id)+'/edit',
      data={'body': body_markdown,
            'comment': 'removed '+tag+' tag',
            'tags': ' '.join(tags),
            'title': title,
            'access_token': token,
            'site': site,
            'key': key
            }
        )