I recommend a clean install of Windows 2000. You can then use Ideal Migration to transfer accounts, passwords, permissions, shares, etc. You can also use Resource Kit tools and some freeware, but these don't do as complete a job.
Microsoft Knowledge Base Article 298107 contains the following summary:
This article describes how to upgrade your Windows NT Server version 4.0 to Windows 2000 Server.
If you are currently running Windows NT Server 4.0, you can upgrade to Windows 2000 Server. If you are currently running Windows NT Server 4.0 Terminal Server Edition (with Service Pack 4 or later), you can upgrade to Windows 2000 Server Terminal Services, which is a component of Windows 2000 Server, Windows 2000 Advanced Server, and Windows 2000 Datacenter Server.
The following information outlines the steps that you must take to prepare your computer before it is upgraded to Windows 2000 Server, as well as the steps to begin Setup.
NOTE: You can upgrade your computer by using either the Windows 2000 Server CD-ROM or a network server.