I had the issue of when a post started off with multiple short lines, the lines would run together since html is stripped, so the end of one line was then flush against the beginning of another line. I saw someone else post about this somewhere while looking for a solution and saw your reply to them... I solved it on my end by using the following and thought maybe you'd be interested in implementing it... I used the following prior to the stripping of the html.
$content = str_replace(array("\n","\r","\r\n","<br>","<br />","<p>"), ' ', $content);