Microsoft, Exchange, 2003 & 2007, Hub transport server is not working with Exchange 2003

Hi All,

I am facing an issue with a new Exchange 2007 Installation in a coexistence environment with Exchange 2003. I had earlier installed Exchange 2007 after making all the necessary changes in the domain. Domain already has an Exchange 2003 server.
Here is what I did in order
1. Created Windows 2003 x64 Standard Edition with SP2.
2. Installed Dotnet Framework 2.0 and Windows Powershell.
3. Ran following commands on the new Windows 2003 machines in following order:
setup /preparelegacyexchange permissions
setup /prepareAD
setup /prepareDomain
4. After that I installed the following roles on the server: Mailbox, Hub Transport, Client Access.
After the installation was complete, I tried to access the OWA site of Exchange 2007 and that didn't work. There were some issues with the IIS configuration, so I removed it and reinstalled, I also had to remove the Client Access Role and then installed it back. But that didn't fixed the issue.
So i uninstalled Exchange 2007 completely but running the setup. In the process of removing it, I removed the routing group connectors from Exchange 2003 System Manager which were created by Exchange 2007 setup for mailflow. and deleted the public folders directly from Domain Configuration partition as exchange Management console wasn't letting me remove it. After it was removed. I fixed the IIS issue. and reinstalled everything (Exchange 2007). But the Hub Transport Role didn't work. I thought there might be some issue with the registry of the Windows Server that might be conflicting with the Exchange configuration.

So I removed it again using the same procedure that I did before, and rebuilded the entire Windows Server system and installed Exchange 2007 from scratch. Now again the Hub Transport Server is not working. The Microsoft Exchange Transport Service is faling again and again.

I am getting the following three Error messages in Event Viewer:
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Event ID: 1009

The Microsoft Exchange Mail Submission Service is currently unable to contact any Hub Transport servers in the local Active Directory site. The servers may be too busy to accept new connections at this time.

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

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Event ID: 7002

Database Transport Mail Database is already in use. The service will be stopped. Exception details: Microsoft.Exchange.Isam.IsamFileAccessDeniedException: Cannot access file, the file is locked or in use (-1032)
   at Microsoft.Exchange.Isam.?A0x56eb15c6.HandleError(Int32 err)
   at Microsoft.Exchange.Isam.Interop.MJetInit(MJET_INSTANCE instance)
   at Microsoft.Exchange.Transport.Storage.DataSource.InitInstance()
   at Microsoft.Exchange.Transport.Storage.DataSource.OpenDatabase()
   at Microsoft.Exchange.Transport.Storage.Messaging.Database.AttachInternal(String path, Boolean wipe)
   at Microsoft.Exchange.Transport.Storage.Messaging.Database.Attach()

For more information, see Help and Support Center at
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Event ID: 491

edgetransport (5944) Transport Mail Database: An attempt to determine the minimum I/O block size for the volume "D:\" containing "D:\Program Files\Microsoft\Exchange Server\TransportRoles\data\Queue\" failed with system error 5 (0x00000005): "Access is denied. ".  The operation will fail with error -1032 (0xfffffbf8).
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I performed these steps as the Hub Transport Service is failing again and again:

http://technet.microsoft.com/en-us/library/bb125177.aspx 

I created the queue database again at a new location. One thing that I noticed is that in the default location of the Queue Database there were no files by name of  "Mail.que and Trn.chk " where as according to the document it should be there.
Even after creating a new queue database directory these two files were not created. So I am actually stuck at this point. I have an Exchange 2003 in working condition, and have an Exchange 2007 server on which the Microsoft Exchange 2007 service stops automatically after five minutes and it is not able to send and receive emails at all. I am able to start the service from the services panel but it will fail as soon as I will try to send an email from Exchange 2007 Owa or Outlook 2007. before it fails a warning message is generated in the Event Viewer indicating that the Mail submission service is currently busy and could not accept emails at the moment, after this error message, the above mentioned three error message comes up and I have Microsoft Exchange Transport Service in stopped condition.

Please help in this regards, every help would be highly appreciated. I know I have written a pretty long topic. But I want to provide as much information as I can to resolve this issue.

Thank you very much.