Personally, I would keep Calibre out of the process, if you can find another way around.
If you have a double </p><p> tag, a simple search & replace can change them to a single one, for example.
The indent would be handled in the style sheet. For a plain <p> you might do this:
p {
margin-top:0.0em;
margin-bottom:0.0em;
text-indent:1.0em;
text-align:justify;
}
You can see (and are welcome to borrow or adapt) my style sheet at
http://notjohnkdp.blogspot.com/