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These issues have been solved so I wanted to post up the solutions for anyone else that may need help.
I had a couple different issues going on and this is what solved them:
Saving projects from Mobile Project Center:
-Mobile folder has only Anonymous Authentication enabled.
-Admin folder has only Basic Authentication enabled.
-Content folder has only Anonymous Authentication enabled.
-Grant the IUSR account full control to the Mobile folder.
-Delete any existing projects from the Projects folder.
-Before attempting to use Mobile Project Center after making these changes, close and reopen the application.
After applying these settings, I was still getting directory access errors through the browser application. After granting write/modify permissions to the machine's "Users" role to inetpub/wwwroot/ArcGIS/mobile folder, these issues were resolved and everything worked fine.
Also, I was not aware of this thread until after I solved my issues, but would have been a good place to look:
Downloading projects/Connecting to server from ArcGIS Mobile on Juno:
At first the Juno would not connect to the server when "Secured Server" checkbox was checked. If I left it unchecked, I could download a project with a secure service (after entering token credentials) and get data, but when the project opened, I would get a "Error opening mobile cache" message. It turns out our SSL certificate (Thawte) was not validating properly on the server (though it appeared to be fine in the web browser). A check with this tool:
and installation of intermediate certificate:
solved the issues for the Juno. After installed the intermediate certificate, the Juno is able to connect with "Secured Server" checked and download/open the project.
Posting updates to server:
Posting updates to the server was failing because I had the geodatabase version used in the mobile service set to protected instead of public, so the user in the service did not have edit permissions on the service.
Hope that helps someone, not an easy task to get set up!