Regarding the page number question: you'll find an option to enable a page number field in Journal Management -> Setup Step 4.3. After you enable this, Editors will be able to enter page numbers for each article from the Issue's Table of Contents management page. This page information will subsequently be displayed in the Article & Issues XML export file, in the <pages>...</pages> tag for each article.
Recent versions of OJS (2.3.3+, IIRC) also include a Citation Markup Assistant that can be used by Editors to extract, parse, and edit reference lists/citations included by Authors. More information on this feature can be found from the third point here
. Most importantly, you can use this feature to semi-automatically convert your articles' reference lists to NLM 2.3 or 3.0 XML, which can then be copy&pasted into any NLM file going to PubMed/PMC. We'll be planning better integration with our various export plugins in the future.
Otherwise ... we'd definitely like to support PMC deposit more fully. I'll be asking our lead developer what we're planning in that regard in the future, and will try to get back to you soon.