So I tried the approach of letting the upgrade make the changes to my existing web.config file.
At first I got a permission error and had to set NETWORK SERVICE permissions.
I updated the permissions and ran the upgrade again. Here is what I got.
Upgrading DotNetNuke
Current Assembly Version: 04.09.01
Current Database Version: 04.05.05
Upgrade Status Report
00: - Upgrading to Version: 4.9.1
00:00:00.015 - Executing Script: 04.06.00.SqlDataProvider Error! (see 04.06.00.log for more information)
00:00:00.609 - Executing Script: 04.06.01.SqlDataProvider Success
00:00:00.640 - Executing Script: 04.06.02.SqlDataProvider Success
00:00:00.640 - Executing Script: 04.07.00.SqlDataProvider Error! (see 04.07.00.log for more information)
00:00:01.062 - Executing Script: 04.08.00.SqlDataProvider Success
00:00:01.234 - Executing Script: 04.08.01.SqlDataProvider Error! (see 04.08.01.log for more information)
00:00:01.453 - Executing Script: 04.08.02.SqlDataProvider Success
00:00:01.500 - Executing Script: 04.08.03.SqlDataProvider Success
00:00:01.500 - Executing Script: 04.08.04.SqlDataProvider Success
00:00:01.515 - Executing Script: 04.09.00.SqlDataProvider Error! (see 04.09.00.log for more information)
00:00:01.609 - Executing Script: 04.09.01.SqlDataProvider Success
00:00:02.265 - Performing General Upgrades
Upgrade Complete
Click Here To Access Your Portal
When I tried to access the portal I got this error.
Server Error in '/' Application.
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Object reference not set to an instance of an object.
Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code.
Exception Details: System.NullReferenceException: Object reference not set to an instance of an object.
Source Error:
An unhandled exception was generated during the execution of the current web request. Information regarding the origin and location of the exception can be identified using the exception stack trace below.
Stack Trace:
[NullReferenceException: Object reference not set to an instance of an object.]
DotNetNuke.Security.Membership.AspNetMembershipProvider.GetUserCountByPortal(Int32 portalId) +9
DotNetNuke.Entities.Portals.PortalInfo.get_Users() +28
DotNetNuke.Entities.Portals.PortalSettings.GetPortalSettings(Int32 TabId, PortalAliasInfo objPortalAliasInfo) +1726
DotNetNuke.Entities.Portals.PortalSettings..ctor(Int32 tabId, PortalAliasInfo objPortalAliasInfo) +76
DotNetNuke.HttpModules.UrlRewriteModule.OnBeginRequest(Object s, EventArgs e) +2165
System.Web.SyncEventExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() +68
System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously) +75
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Version Information: Microsoft .NET Framework Version:2.0.50727.3053; ASP.NET Version:2.0.50727.3053
Thanks for any ideas on what I could have done wrong.