I had a chance to review the docs you gave me. Alas, given where I stand pre AERA (and post Gary), I don't think I will be able to make it tomorrow. So, for what its worth, here are my comments. They range from the general to the specific....
1) Fantastic idea. Much needed. Wish I had it. The only conceptual issue you may face is that a lot of what this needs to do is content management/work-flow type functionality that frankly is desperately needed at TC in other contexts. So the back end of Doc.Life feels like it can/should be used for other purposes (e.g. File content management ala Xythos). A good thing, except as it raises the risk of scope creep.
2) Of the capabilities you describe, the most compelling to me are: file posting and sharing (which helps students back-up and reduces email storage costs); tracking of deadlines and milestone; tagging of faculty expertise by methodology and research interests; doctoral student portfolio / personal Web presence for job search, working and conference papers, etc.; and collaborative /social networking space for doctoral seminar groups and cohorts.
3) Not listed (I think), but also valuable, are: linkages into the library systems for management of citations and annotated bibliographies; promotion of funding opportunities and deadlines; ability for dissertation committee members at CU to be equal citizens.
4) As you probably have discovered there are definitely programs/theories about doctoral success that could frame its functionality. I imagine Spencer has one, perhaps with Web tools. From my perspective, at the risk of being low-brow -- nailing the short list of top 5 pains of students and their advisors is much more impactful than nailing any particular model of student success. But I am a techie :-)
5) The feature creep issues arises when I think about how cool this would be in supporting doctoral research (survey design examples, available dataset links for exploration, IRB info, etc.); eventual job search; and the administrative elements of the process.
Hope these comments.