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Synchronization fail in all downstream server, 4 layers of WSUS server - Can it be fixed?

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Hello support friends. Following is a diagram of our WSUS setup. Other than the top server RPAWSUS01 and RPAWSUS02, the rest are in different geographic location. This was done not to kill the network when updates are approved once a month. Rough total clients serverd by each server is given below. Clients are targetted using AD group policy.

A rough estimate of number of clients that each server is supporting is as follows.

RPAWSUS01 = 215 Clinets, (Primary server, has one downstream server called RPAWSUS02)
RPAWSUS02 = 3815 Clients, (Downstram server in replica mode to RPAWSUS01, has two downstream server called LIVWSUS01 and CRGWSUS01)

LIVWSUS01 = 3891  Clients, am server in replica mode to RPAWSUS02, has 6 downstream server)
FRFWSUS01 = 588 Clients,(Downstream server in replica mode to LIVWSUS01)
FRFCHCWSUS01 = 259 Clients,(Downstream server in replica mode to LIVWSUS01)
BNKWSUS01 =837 Clients, (Downstream server in replica mode to LIVWSUS01)
CTNWSUS01 = 1036 Clients, (Downstream server in replica mode to LIVWSUS01)
CMDWSUS01 = 188 Clients, (Downstream server in replica mode to LIVWSUS01)
BOWWSUS01 = 230 Clients, (Downstream server in replica mode to LIVWSUS01)

CRGWSUS01 =   1530 Clients, (Downstream server in replica mode to RPAWSUS02, has 2 downstream server)
TCHWSUS01 =  434 Clients, (Downstream server in replica mode to CRGWSUS01)
BALWSUS01 =  126 Clients, (Downstream server in replica mode to CRGWSUS01) 

Updates that are approved automatically to all clients when they arrive are Critical Updates. We also approve all Security Updates, Updates and Deffinition Updates once a month once they have passed the trial groups. Our environement is set as Prod 1 and Prod 2. 3rd week of the month updats are approved for Prod 1, and next week Prod 2 gets the same set of updates approved.

On the primary server RPAWSUS01 following is the status:
Unapproved updates: 51
Approved updates: 9428
Declined Updates: 25122
Computers: 215
Computer Groups: 62

Issue: In server RPAWSUS02 the status is as follows,
Unapproved updates: 23438
Approved updates: 9428
Declined Updates: 2098
Computers: 3815
Computer Groups: 62

Similar disparity exists in all the downstream servers. None of the dowstream servers finish sync, they his 99% and time out. But, when I approve an update during the 3rd and 4th patching week, the clients sitting at different geographical location are being offered the approved updates.

I have same error as follows in all the downstream servers, except the primary server RPAWSUS01

SqlException: Timeout expired.  The timeout period elapsed prior to completion of the operation or the server is not responding.
at System.Data.SqlClient.SqlConnection.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.SqlDataReader.ReadInternal(Boolean setTimeout)
   at Microsoft.UpdateServices.DatabaseAccess.DBConnection.ReadOneRow()
   at Microsoft.UpdateServices.Internal.DataAccess.HideUpdatesForReplicaSync(String xmlUpdateIds)
   at Microsoft.UpdateServices.ServerSync.CatalogSyncAgentCore.ProcessHiddenUpdates(Guid[] hiddenUpdates)
   at Microsoft.UpdateServices.ServerSync.CatalogSyncAgentCore.ReplicaSync()
   at Microsoft.UpdateServices.ServerSync.CatalogSyncAgentCore.ExecuteSyncProtocol(Boolean allowRedirect)

The system of servers worked for a month in terms of syncing etc. I understand, possibly by mistake theDrivers Classification was ticked in the primary server. Metadata info possibly bloated its DB. Since then, I belive this sync issue started.

We normally synchronize the following classification: Critical Updates, Definition Updates, Feature Packs, Security Updates, Service Packs, Update Rollups and Updates.

Servers are all Vmware guests with specs as follows:

Windows Server 2008 R2 Standard with SP1 (64 bit)
4 CPU assigned at 2.53 GHz
12 GB RAM
C Drive for OS
D Drive for WSUS contents (300 GB, among wihich about 95% is filled up)

I understand this is a large number of servers, but I think one fix may fix all the rest of the servers. Can someone kindly point me to a start? I have run WSUS DB indexer script from the Scripting Guys mainly when the systems were all put in place. It still runs OK, but now when I try to run the WSUS Clenup wizard, it never actually starts or seems to timeout.

I am happy to provide more logs etc, but I need to know which servers to start looking at primarily.

Thanks


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