Re: Cannot find the Site Settings link
So in follow up I think what happened is the Setup page detected that the Data folder is writable so it allowed you to proceed with setup but because child objects were not writable errors occurred in creating the search index files and this interupted normal creation of default data before it could complete.
I definitely need to implement some handling for this kind of thing so it can recover gracefully and finish creating the data after the problem is corrected.
Joe