it's a complex setup, I grant you.
I suppose I'd start by scaling it back and listing my needs.
1) Users can login and only download their content.
2) No one else can see their content.
I wouldn't even use Multisite for that. I'd use Custom Post Types and then grab http://wordpress.org/extend/plugins/user-specific-content/ to hide each thing.
Or heck, have one master page with the downloads, everyone goes there, each person only sees their own content.