I was have WSS 2.0 and then I upgraded to WSS 3.0 and the old instalation database was SQL 2000, now I have another SQL Server instance called:server_name\MICROSOFT##SSEE .

After upgrade every thing works fine and our team started to use the portal and we sent lot of documents and make lot of activities on it. The problem started after installing Windows updates the website suddenly stopped and giving me an error

"Cannot connect to the configuration database"

If I tried to open SharePoint Products and Technologies Configuration Wizard it is gives me a strange error says: "An exception of type Microsoft.SharePoint.PostSetupConfiguration.PostSetupConfigurationTaskException was thrown. Additional exception information: SharePoint Products and Technologies cannot be configured. The current installation mode does not support SKU to SKU upgrades because there exists an older version of Windows SharePoint Services that must be upgraded first "

At this post:http://stackoverflow.com/questions/114398/iis-error-cannot-connect-to-the-configuration-database/249494#249494 the guy of the second answer have the same problem and he suggested a solution but I don't understand well. I tried as he suggested to make the identity of the app pool of the SharePoint web site as "IWAM_server_name " after that the error changed as he said and I web site give me "Server Application Unavailable " and when checked the Event Viewer at the server I found that ASP.NET 2.0 give this exception: "Could not load file or assembly 'System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a' or one of its dependencies. Access is denied ." and I don't know how to solve this problem.

I'm really want to make my web site working because our team really need these documents and its stuff.

I hope I will find some one to help me.