The problem is that you appear to actually
have only one paragraph. That's why only the very first line is being properly indented. The code is only
simulating paragraph breaks using <br /> tags. Also note that the "text-indent" attribute cannot be applied to <span> tags... it has no effect.
I'm afraid you have your work cut out for you. You need to overhaul the code so you have individual paragraphs, instead of giant paragraphs that are divided with <br /> tags.
I've run into those situations before. They suck. No choice but to dive in and start rewriting. You can attempt to replace those <br class="calibre4"/> tags with </p><p class="calibre2> for starters, but always keep a good backup because that kind of major Find and Replace surgery may very well break other things badly.