Hi Dan,
I wouldn't use SharePoint for this since it will be a configuration nightmare (what happens when an employee changes managers, etc.). I'd use a Web service and SQL (or just do e-mail for now). We have a Web service (Database Accelerator) that supports easy connection to a SQL database. We have some limited roles-support now and are adding more for a June release. This probably doesn't fit in your timeline, but it's quite a bit of work to do this on your own. SharePoint doesn't currently support fine grained per document permissions. There is better support coming later this year (or so I have heard). I would do it in e-mail for now. That's simple and cost effective.
Patrick Halstead [InfoPath MVP]
InfoPathDev
Patrick Halstead
Project Manager at Qdabra