I can appreciate the motivation to keep everything in one central place, but IMHO this is "overloading" (in the functional, not literal sense) what OF does.
OmniFocus is for managing tasks, thats about it.
There are several choices to store other things and have them "related" to the tasks.
I think mail.app does a good job with email (it could be better). But when you clip an email into OF, there is a link in the clipped text is a link to the "original message". Once I've captured the attachment, or replied to the email, it then goes in an archive.
For notes and reference material you can keep a pretty sane set of Finder folders - (you can drag a link to a folder into a note), or other files - and not embed them (avoid inflating the OF DB).
This does result in three places: Tasks, Correspondence, Reference/Resource
I use a combination of Finder and Journler for for files and notes.
If the project is long term and has lots of notes involved, I use Journler which has great tagging features, and is faster and cleaner to search than a bunch of text files. It can manage a ton of files without bloating, because it basically manages a repository ala the iTunes music folder.
If the project is mostly about some files and a produced result with few notes, then I will just use a folder in my ~/Projects folder (my root folder for all projects).
I've created a script that can create an entry (with link in OF notes) in Journler for a task:
http://forums.omnigroup.com/showthread.php?t=7568
And there is a script I made for Journler that creates an embedded OmniOutliner Document (still a favorite for note taking and brainstorming).
For me the only improvement to OF would be to assign a global "project folder" to a project, and have that be available from within any task. This is pretty particular to my own workflow though and would not make a good general feature (I can implement it in a script come to think of it).
So not exactly the advice you were maybe looking for. If you like the interface OF provides, and feel the Finder is a little to chaotic for you, I would check out Journler, its a great app. (it won out in my head to head evaluation of the apps in its class).
-Preston