MSSQL Security and or Trust Issues

I have a huge problem and woulod really appreciate some direction on how to fix the following problem.

Back in December my Win2k3 Server that runs my MSSQL Server crashed. I tried repairing the OS to no avail. The only solution that seemed to work was a complete reinstall of 2k3 and SQL. I then attached the databases.
The problem is this. Our ERP software can not access the databases unless the user is in the Domain Admin group. I have tried setting up permissions within SQL to allow everything from individual access to group access.
Right now I have all of my users in the Domain admin group so that they can work. There is no way that I can let this continue for much longer. It is already starting to cause problems. Please help!

Simon