Hi Joe G,
If you're willing to provide me a little support and testing on your end perhaps I would be willing to make the needed changes. If it is simply a matter of detecting some custom server variables and then setting an authentication cookie in mojoPortal that sounds like it would be pretty easy. We actually have a built in tool to display the current server variables under Administration > Advanced Tools > Developer Tools > Server Variables
But since I don't have a Shiboboleth environment I would need you to tell me what the server variable names are and what they mean and which ones when detected should be used to decide whether to set the auth cookie to log the user into mojoPortal.
Then I could code it up and push it to our source code repository and you could test it on your end.