Hi,
Similar thread is going on ...I would like to suggest same steps.
https://www-secure.symantec.com/connect/forums/upgrade-sep-11ru4old-server-121-ru1new-server-another-server#comment-6580141
I would suggest upgrade existing SEPM & SEP clients from RU6 MP3 to SEP 12.1 RU1.
After successful upgrade move your SEPM to another server by following disaster recovery.
http://www.symantec.com/docs/TECH160736
Check following article to know how upgrade process works.
https://www-secure.symantec.com/connect/articles/sep-11x-sep-121-upgrade-process-graphical-overview
You can download also.
https://www-secure.symantec.com/connect/downloads/sep-11x-sep-121-upgrade-process-graphical-overview
There are couple of options available to move SEPM from one server to another server.
For more details check this thread
https://www-secure.symantec.com/connect/forums/sep-11-full-migration-one-server-another#comment-5506111
Note : Replication is an option, but its better not to go for that. Because if you do replication and remove the old server that is the Primary SEPM, in future if you want to do replication you will not be able to do so.
I hope this information will help you to decide next course of action !!!