I don't think that's going to help you.
<pre> tag preserves whitespace. Adding pre to replace_tags_with_spans would cause it to be replaced with <span class="pre">.
Now all the text inside that span does
not preserve whitespace and it's all going to be one text block now.
Without seeing some of these stories (SFW story URLs only please), I can't help any more than that. And FYI, I don't expect to be able to help much anyway for stories formatted with <pre>