Thanks for the replies Rizla. Scripts are left-justified except for dialogue, which is left-justified within a narrower column in the centre of the page. The problem is less about not being able to convert them (which would only be an issue with a relatively small number of especially poor-quality scans) than not wanting to lose the original formatting (most notably pagination). That's also why PDF is the most suitable format, since .html documents don't have pages at all.
a random example that's roughly representative of most of the scripts I'm talking about.