FYI, the reason we went with frames for article viewing is because we need to support reading tools in a plugin environment such as when using PDFs for articles.
Section navigation for articles is tricky; there's nothing of the sort currently included in OJS, although we're working hard on integrating support for XML-based articles which will make this sort of feature much easier to implement. Off the top of my head, I'd suggest looking into your HTML and seeing if you can identify a standard tag used for article section headings. You can use regular expressions to parse these out of your HTML article galleys and generate links into the article. It will take some PHP and regular expression expertise, however.
Open Journal Systems Team
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