Glad to hear that you are interested in OJS! Please see below:
1. Can we / how do we alter the manuscript submission numbering system to assume our formula (yr/arrival order, eg, MS0923, MS1046, MS1101)?
To do this internally for the submissions as they are tracked through the system, you would have to make some code changes. There is a rationale to the submission ID naming convention in OJS -- Editors and Journal Managers are able to look at any given file and understand where it falls within the submission's history, and which version of the file for that particular stage it is. However, you do have control over how your submissions are named/presented after publication by using public identifiers.
2. It is often the case that authors need to make changes to a paper before it goes into the review system. What provision is there in the OJS submission system to ‘quarantine’ papers until they meet our requirements, and to ensure the revised submission has the same manuscript number as the original and is the version used?
You can always request revisions before the submission is sent to reviewers: during the Review process, but before any reviewers are assigned, the Editor can choose between the Revisions Required or Resubmit for Review options; the Revisions Required option will keep the submission open, and will allow the Author to resubmit a file to the submission (which will increment the manuscript ID), whereas the Resubmit for Review option will decline and archive the submission, mandating that the Author start the submission process anew (presumably taking the Editor's suggestions to heart). There isn't a specific quarantine process per se, but the system should be flexible enough to handle what you want it to do.
3. Is it possible to alter/customise the editing/production flowchart and system?
Again, the system is quite flexible and can handle many, many different types of review and editing processes. Further details on your current workflow would be needed to give a more detailed response.
7. Can the submission system handle multiple email addresses of authors?
Not currently, no, but this may be added in the future if there is interest in such an extension.
8. JoP does not use blind review. Can OJS be customised to indentify authors before papers go for review?
This would require some code changes, but yes, this could be done.
9. How does it distinguish the contact author for review and for publication? (Often these are different.)
OJS differentiates between authors as active submitters and authors as part of the article metadata. The submitting author must be enrolled within OJS to submit an article, but can add other author information as part of the submission process. These authors are not enrolled as users -- they are just included as bits of metadata, however the submitting Author can also choose one of the other authors to be the principal corresponding author for editorial correspondence. A submitting Author can even submit an article that s/he has nothing to do with on behalf of others (a handy tool for Editors to quickly add content as need be).
This distinction can be confusing to describe, although it's normally clear for the authors; my recommendation is to try out OJS on our demo install (http://pkp.sfu.ca/ojs/demo/testdrive/index.php/;
username: admin; password: testdrive) and go through a number of article submissions.
11. How do we convert final files to HTML for posting along with .pdf?
Any number of a million ways.
OJS doesn't currently handle galley creation (unless you happen to be converting submissions to XML, eg. NLM, as part of your workflow process, in which case take a look at the XML Galleys plugin). We do plan on supporting a full XML galley generation/gestation/production process in the future, but until then you'll have to create your own. It all really depends on how you are handling your submissions: what you are accepting as formats for both submissions, images, figures, tables, etc., and how much time you spend or want to spend converting them into other formats. Searching the net would be a good start for finding information on eg. clean PDF-> or Word->HTML conversion options.
Let us know if you have any other questions!