I am in the process of updaing a site from 3.2.2 to 5.1.4.  I have successfully followed this process for three other sites:

3.3.7 -> 4.4.1 -> 4.6.2 -> 4.8.4 -> 5.1.2 -> 5.1.4

I have successfully reached 4.8.4, although in doing some research, I did have two errors (4.0.0 and 4.3.5)  and these may be causing my current woes.  The first one is the 4.0.0.log error which essentially reads: (I won't post the whole thing)

System.Data.SqlClient.SqlException: Cannot resolve collation conflict for equal to operation.
   at System.Data.SqlClient.SqlConnection.OnError(SqlException exception, Boolean breakConnection)
   at System.Data.SqlClient.SqlInternalConnection.OnError(SqlException exception, Boolean breakConnection)
   at System.Data.SqlClient.TdsParser.ThrowExceptionAndWarning(TdsParserStateObject stateObj)
   at System.Data.SqlClient.TdsParser.Run(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj)
   at System.Data.SqlClient.SqlCommand.RunExecuteNonQueryTds(String methodName, Boolean async)
   at System.Data.SqlClient.SqlCommand.InternalExecuteNonQuery(DbAsyncResult result, String methodName, Boolean sendToPipe)
   at System.Data.SqlClient.SqlCommand.ExecuteNonQuery()
   at DotNetNuke.Data.SqlDataProvider.ExecuteADOScript(String SQL)
   at DotNetNuke.Data.SqlDataProvider.ExecuteScript(String Script, Boolean UseTransactions)

ALTER PROCEDURE dbo.aspnet_UsersInRoles_RemoveUsersFromRoles

and later:

System.Data.SqlClient.SqlException: Cannot resolve collation conflict for equal to operation.
   at System.Data.SqlClient.SqlConnection.OnError(SqlException exception, Boolean breakConnection)
   at System.Data.SqlClient.SqlInternalConnection.OnError(SqlException exception, Boolean breakConnection)
   at System.Data.SqlClient.TdsParser.ThrowExceptionAndWarning(TdsParserStateObject stateObj)
   at System.Data.SqlClient.TdsParser.Run(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj)
   at System.Data.SqlClient.SqlCommand.RunExecuteNonQueryTds(String methodName, Boolean async)
   at System.Data.SqlClient.SqlCommand.InternalExecuteNonQuery(DbAsyncResult result, String methodName, Boolean sendToPipe)
   at System.Data.SqlClient.SqlCommand.ExecuteNonQuery()
   at DotNetNuke.Data.SqlDataProvider.ExecuteADOScript(String SQL)
   at DotNetNuke.Data.SqlDataProvider.ExecuteScript(String Script, Boolean UseTransactions)

ALTER PROCEDURE dbo.aspnet_UsersInRoles_AddUsersToRoles

The error from 4.3.5.log is:

System.Data.SqlClient.SqlException: Column names in each table must be unique. Column name 'LastUpdated' in table 'dbo.Folders' is specified more than once.
   at System.Data.SqlClient.SqlConnection.OnError(SqlException exception, Boolean breakConnection)
   at System.Data.SqlClient.SqlInternalConnection.OnError(SqlException exception, Boolean breakConnection)
   at System.Data.SqlClient.TdsParser.ThrowExceptionAndWarning(TdsParserStateObject stateObj)
   at System.Data.SqlClient.TdsParser.Run(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj)
   at System.Data.SqlClient.SqlCommand.RunExecuteNonQueryTds(String methodName, Boolean async)
   at System.Data.SqlClient.SqlCommand.InternalExecuteNonQuery(DbAsyncResult result, String methodName, Boolean sendToPipe)
   at System.Data.SqlClient.SqlCommand.ExecuteNonQuery()
   at DotNetNuke.Data.SqlDataProvider.ExecuteADOScript(String SQL)
   at DotNetNuke.Data.SqlDataProvider.ExecuteScript(String Script, Boolean UseTransactions)

/* Add LastUpdated Column to Folders */
/*************************************/

ALTER TABLE dbo.Folders ADD
 LastUpdated datetime NOT NULL CONSTRAINT DF_Folders_LastUpdated DEFAULT getUtcDate()

Now, question #1 - Can I go back and run the 4.0.0 SQL provider script, or has some other update changed that procedure?  As for the 4.3.5 error, the column already exists, so is this acceptable?

The primary pain is during the 4.8.4 -> 5.1.2 upgrade.  Everything works fine here until the script starts to update the HTML_Community_05.01.03_Install module.  This fails with an error, no log.  Everything else continues to install (this is the default upgrade package), and when it gets to the FckHtmlEditorProvider_02.00.04_Install, an  Application error indicates that the Thread was being aborted.  The following error is shown:

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:

[ThreadAbortException: Thread was being aborted.]
       System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously) +486
       System.Web.ApplicationStepManager.ResumeSteps(Exception error) +501
       System.Web.HttpApplication.System.Web.IHttpAsyncHandler.BeginProcessRequest(HttpContext context, AsyncCallback cb, Object extraData) +123
       System.Web.HttpRuntime.ProcessRequestInternal(HttpWorkerRequest wr) +379

This is still going against a SQL2000 database.

Any help on this would be great!

Cheers
Dave

Please make sure, using a case insensitive collation for the upgrade, during the upgrade, server collation should be same as database collation.

Besides, SQL 2000 is no longer supported in DNN 5.2 and there are known issues using it with DNN 5.1.x

Dave,

upgrading a site from a very early version like 3.2 to current, I always prefer to perform locally on my own machine with SQL Server and IIS under my control. Collation issues occur, if two columns use different collation, in most cases this happens if DNN database collation and server collation don't match, which is used for temp tables. This should at least solve the user upgrade issues. you might ignore the folder issues, AFAIR this has been corrected a number of times in multiple versions and should be fine, after you passed them all.

Regarding module upgrades, the result should be logged in DNN EventLog.