Wrong permissions set in Windows Server 2003 (64 bit)-cannot access server

Hi
We’ve been trying to switch our server over from managing client computers as a workgroup to a domain. Everything was working well but then we started applying permissions to folders. Now the Administrator can’t log on to the admin account and Active Directory is not starting up the services needed for the server to function. We cannot access security permissions, group policies, cannot connect to router (& internet), access internal network or files on server. Have tried to restore backup but access is denied. Likewise cannot copy files to usb drive etc

Does anyone know if its possible to restore permissions to default settings via a command line program or if there are any tools in Windows Server that can help us with this?