I found this link, which is really useful:

http://webborg.blogspot.com/2007/06/reinstalling-sharepoint-wss3-to-run.html

Repeated here for ease of searching


Recently I was fixing on one server an installation of Windows SharePoint Services that has gone wrong. Even though we’ve had SQL server 2005 installed correctly, WSS3 installed its own Windows internal database (##SSEE) and started using it. I thouhght a simple uninstall and reinstall of WSS would do the trick. But it didn’t. After uninstalling and trying to reinstall WSS3 at the beginning didn’t even offer the option to configure it to SQL server (the step in WSS configuration where is asking you which is the location of configuration database,…).

After a couple of retries (also uninstalling SSEE and a lot of reading on the web to my horror I’ve found one sentence "you’ll need a clean install of Windows Server 2003."

.

This was a bit tough because of existing users and some other parameters. After digging a bit deeper and combining knowlege of couple of experts’ blogs I’ve managed to successfully reinstall WSS3 without Windows Internal Database (SSEE) and into SQL server 2005.

Before I write how I did it, let me clear that this solution worked for me. I’m presuming that you don’t have anything else installed in SSEE and I’m not responsible for any errors that might happen if you’re following the same procedure. So please before making anything on a production server – backup, backup, backup. This procedure includes messing with Windows registry!

Here goes:

1. Copy all the SharePoint Sites to another temporary folder
Using

stsadm -o backup -url http://<site_collection_url&gt; -filename <location and filename>

copying backup files to new server and

stsadm -o restore -url http://<site_collection_url&gt; -filename <location and filename>

on the temporary server worked the best. It kept all the relations and all the custom formatting on all the sites.

2. If these are productions sites modify DNS or forwarding to point to the temporary server

3. Here’s where the "fun" begins: Delete all the SharePoint Web applications

4. Uninstall Windows SharePoint Services through Control Panel

5. Uninstall Windows internal database (##SSEE)
Connex’ Copper Coins has it described in his blog here. Just in case I’m writing a short ressume:

Under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall click different GUIDs untill in the right pane you see under "Display name" Microsoft SQL 2005 Embedded Edition". Under that registry copy the value under "UninstallString". Run the command prompt window, paste the command AND add "CALLERID=OCSETUP" at the end of commend line. For example: MsiExec.exe /X{BDD79957-5801-4A2D-B09E-852E7FA64D01} CALLERID=OCSETUP.EXE.

(ressumed from Connex’ Copper Coins)

6- Delete all files and folders under %windir%\SYSMSI\SSEE

7. delete all and folders files under %Programfiles%\Common Files\Microsoft Shared\web server extensions\12

8. Using reged backup and delete in registry everything under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\Web Server Extensions\12.0\

9. The previous step also deleted the "Server language" entry. so Using notepad create a .reg file with the following text:

Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\Web Server Extensions\12.0\ServerLanguage]
"1033"=""

and run it to restore the "Server Language" entry needed for Windows SharePoint Services installation.

With that I have removed every trace (or at least enough) of Windows SharePoint Services 3.0 from the server. Now I was able to re-run the WSS 3 setup and and it offered me the option for nstalling it into SQL server 2005 and without SSEE.

This is how you can have it done without making a clean install of Windows Server 2003.

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