Can Microsoft Project be used without Sharepoint Server

I've seen this happen when the server is low on resources (slow CPU or not enough RAM - you should have at least 2GB). Also sometimes when there are network issues as I believe this service tries to contact Microsoft for some reason. And also sometimes just because that's what it does...

This should be fixable by increasing the service start time-out. Go to KB article 824344 and search for 'time-out'. Make the timeout at least 5 minutes, maybe 10 if you still have problems and it should work correctly!

By the way, trying to change the account the service uses isn't recommended unless you do it through stsadm or SharePoint Central Admin.

Manage Content and Structure is part of the MOSS functionality. I have to assume that when you uninstalled Project server it deactived the Publishing Feature (sorry I do not have the exact name(s)).

I suggest that you create a new Publishing Collaboration site and see which features are activated. If you do not see Publishing Collaboration sites as one of the options then you will need to repair your SharePoint installation.