IDEAL Migration was designed to migrate objects from one domain to another new and different domain, even the names!
In fact, it can do what you want without any problem, but it's not its default configuration.
First of all, install IDEAL Migration on the **OLD** PDC server (PDC Emulator in fact, your old server running Windows 2000 if you prefer). Fill in your registration key and restart IDEAL Migration.
On the target server, running Windows Server 2003 R2, please edit its boot.ini file and replace /NoExecute=OptIn with /NoExecute=AlwaysOff and restart this server.
In your case, the easiest way is:
-1- Upgrade the AD schema of your EXISTING domain,
-2- Join the new server into the domain,
-3- Make your new server a domain controler of your EXISTING domain,
-4- Copy all the shares, files, folders and permissions onto the new server,
-5- Install DNS on the new server,
-6- Make your old server a member server,
-7- Remove your old server from the domain,
-8- Raise the level of functionnality of your domain to Windows Server 2003,
-9- Rename your new server to use the name of the old one,
-10- Take a coffee!
Here are the main steps:
Step 1: Upgrading the AD schema.
Insert your Windows Server 2003 CD in the CDROM drive of the OLD server, open a command prompt, cd to D:\i386 (if D: is the letter used by your CDROM drive), and type:
Once done, type: adprep /domainprep
Step 2: Joining the domain.
On your Windows 2003 server, make sure the network settings are set to use the"old" server as the DNS server. Then, right click on My computer, select "Properties" then Computer name then Modify and make it a member of your existing domain. Restart it.
Step 3: Becoming a domain controler.
On the new server, run DCPROMO and select New domain controler and then "For an existing domain". At the end, restart it.
Step 4: Migrating your datas.
Launch IDEAL Migration on the OLD server and select Migration assistant in the left pane. Then, in the right pane, click twice on Shared folder migration. Click on the icon with a magnifying glass in front of a PC. In the new window, click on the same icon: this will show you ALL the shares defined on the OLD server. Please, move all the shares you want to migrate in the lower part of the window: no need to migrate Admin$, C$, Netlogon, and so on... Click OK. When back to the window Shared Folder Migration, click "Import Shared Folders", fill in the NetBIOS name of your new server in the To field, set Translation to None, check the options linked to the drive letters and click"Execute". Save the migration project into a file (allowing one to know what options you checked/unchecked) and go!
Once done, please look carrefuly at the log file: there should be NO error.
Do the same with Files and Folders permissions then Printer ports and last Printers.
In all cases, Translation *must* be set to None, meaning: source and target domains are the same.
Step 5: Installing DNS.
If not already done, install the Microsoft DNS Server service on the new server. Once installed, go to Administrative tools / DNS and make sure your internal DNS zone is shown. Once checked, change the network settings of your new server in order to use itself as its main DNS, no backup DNS needed. Restart it.
Step 6: "depromoting" the old server.
On the OLD server, run DCPROMO in order to make it a member server but do NOT check This is the last domain controler. This way, all the FSMO roles will be transfered to your new server. Once finished, restart the OLD server.
Step 7: Removing the old server from the domain.
On your OLD server, make sure the network settings are set to use the new server as the DNS server. Then, right click on My computer, select Properties then Computer name then Modify and make it a member of a dummy workgroup. Shut it down and UNPLUG it from the network.
Step 8: Raising the domain level.
On your Windows 2003 server, go to Administrative Tools / Domains and trusts AD. Right click on your domain name and select Raise level: select Windows 2003.
Step 9: Renaiming the new server.
On your Windows 2003 server, right click on My computer, select Properties then "Computer name" then Modify: you'll be able to change its name back to the one used by the old server. Restart it.
Step 10: Coffee time!
I don't think I need to explain you this step :-)