I think OJS would be good for what you are describing; however, you will most likely want to make some customizations, and you'd probably have to maintain two separate instances of the software if you were to also use OJS for e-Publishing as it is traditionally used.
Have you used the OJS software before? It supports multiple rounds of peer review, and allows for comments to be shared between reviewers, editors and authors. It is also built to provide blind peer reviews (so long as editors are careful to check that identifying information in any uploaded document has been stripped before being passed on). It includes a fair number of prepared emails (which can also be tweaked) which are sent by the system at various times, for example when an author finalizes a submission. It also includes the option to save all submission logs -- for emails and actions -- so that a 'paper trail' for each submission is kept.
Finally: we have had a number of people modify OJS to suit their own workflow purposes, which at times have nothing to do with journals. While we don't support these endeavours in the same way we support OJS and OCS, we are nonetheless very happy to see the software used in this way, and we'll be as helpful as time permits if you have any particular development questions.
If this seems like something your group may investigate further, I would recommend taking a look at the documentation found at http://pkp.sfu.ca/ojs_download
, especially OJS in an Hour, which details the entire system from an end user's perspective; the Technical Reference, which gives a detailed overview for developers; Customizing OJS, which will show you some of the very quick ways you can modify the appearance of the system; and Translating OJS and OCS, which will explain how to make locale (overall language) changes. At least initially, you can probably go far in modifying the system to meet your needs by making changes to the system's locale and template files.
Please let us know if you have any other questions.