Sounds very similar to some of the things I am doing for dotfolio (e-portfolio application). Essentially I am creating a subsite for each e-portfolio owner, and each subsite contains file-storage and web-blogger packages.
I too was unsure of scalability, so I wrote a script that created 1000 e-portfolios, or 1000 subsites. Although it took a long time to create the 1000 subsites, there seemed to be no detrimental effect to performance when hitting a particular e-portfolio subsite. Mind you I didn't test scalability when a number of users hit the application simultaneously. But I doubt acs-subsites will contribute to a drop in performance, if any.
The linking of project tasks and file-storage items sounds very similar to how I'm linking blog entries to file-storage items. I am using the relate and clipboard packages for this. You might want to investigate these packages in COP and dotFOLIO.
