Most straight forward approach....
- Since all users are on the same domain, move all the users from BES Server B to BES Server A. This will leave Server B with no users on it.
- Decommission Server B; blow away the OS and reload everything from scratch. Operating System, Anti Virus, EVERYTHING!
- Then load BES 5.x on Server B using the extra SRP and creating a new BESMgmt5 database on a SQL Server.
- Use the Transporter tool to move your users from Server A (4.1) to Server B (5.x).
- After everybody has been moved off Server A, decommission Server A and reload OS, anti virus from scratch.
- Install BES 5.x on Server A as the High Availability Server. (Don't use the extra SRP as the installation will detect the current BES 5.x install on Server B)
No downtime for your users.
You'll use the SRPs available to you. In fact, you'll have an extra SRP left over in case you want to expand in the future.
You don't have to use the Migration Kit. (Cumbersome at times... just an opinion)