Jason,
I would uninstall it and reinstall the 2010 agent clean - as of now you can't really be sure if the installation was complete or not. Your selection lists, etc should still be OK on your BE server (I'm assuming you have BE running on another server and your 2003 DC has the remote agent).
Do you have the installation media available? Once clean installed, I would either use the bulk update utility to update the agent, or do what you did by copying the RAWS folder from the BE server to the agent server and updating manually.