I've traweled through numerous articles, blogs and other sources, and it appears that you cannot programmatically add a Project level Connection Manager to a package, except through BI studio.

However, the work round is to reference the project level connection, then Instantiate a Package Level connection using the project level connection details.

It also seems that the SSIS Project Class is screwed as you cant open existing projects to add packages as it reutrns an invalid XML error when reviewing the dtproj file you pass int using the OpenProject method.

When completed and tidied up the code to generate a simple package I'll post it for to the community as a starting point for everyone to use.