Darth, I just finished upgrading all 6 of our servers from 4.0.6 to 4.1.3, I didn't install the new "MDS Services and Components" stuff, just the base install "BES and Components" which includes the MDS connection (same as 4.0 MDS). Unbelievably, I didn't encounter any issues with any of these upgrades, they were clean.
Here are my steps I followed for my upgrades, some may not apply to you, but maybe this will help out somewhat:
BES Server 4.1 Upgrade Instructions
1. Assign the xxx8220;serveradminxxx8221; SQL Server role to the "****" SQL login. [SQL Team]
2. Set startup type to Manual for the Lotus Domino Server (LotusDominoData) service
3. Restart BES server to be upgraded.
4. Stop all BlackBerry services on the BES server to be upgraded.
5. Stop the following on all other BES servers:
xxx8226; Domino BES task
xxx8226; Dispatcher Service
xxx8226; MDS Service
xxx8226; Policy Service
xxx8226; Synchronization Service
6. Verify no connections to SQL DB, if there are open connections from BB Managers, drop them. [SQL Team]
7. Backup BESConfig DB to disk file via SQL Enterprise Manager. [SQL Team]
8. Close any open Services windows and run upgrade from \\*****\installs.
xxx8226; Note: If the MDS and Dispatcher services could not be removed allow the setup process to restart the server, and re-run setup.
9. Restart server when prompted, upgrade the DB, and verify upgrade was successful.
10. Do not start the services, however apply the hotfix and restart.
11. Verify functionality.
12. Restart all other BES servers.
13. Remove the xxx8220;serveradminxxx8221; SQL Server role from the "****" SQL login. [SQL Team]
14. Assign xxx8220;rim_db_admin_enterprisexxx8221; BESConfig DB role to xxx8220;****adminxxx8221; login. [SQL Team]
15. Test BES Manager 4.1 login and functionality.
16. Update log sharing folder.
17. Update GSX for new version.
18. Work with Citrix team to enable BB Manager 4.1
19. Send out instructions for BES Manager upgrades
Restoring a previous backup due to failure of SQL DB upgrade:
1. Uninstall upgraded BES from upgrade server
2. Choose to keep the BES data directory, as the BES task was never started and the files remain at the old version.
3. Restart BES server.
4. Close any open Services windows.
5. Install old version from \\****\installs.
6. Restore BESConfig DB from disk file via SQL Enterprise Manager. [SQL Team]
7. Restart all other BES servers.