Hi,
SEP Migration for version up gradation (from 11.x to 12.x)
--> Check this thread
https://www-secure.symantec.com/connect/forums/move-sep-11-new-server-and-then-upgrade-sep-121#comment-8145961
Any challenge from SEP end for endpoint that are under VM environment
--> I don't think so
Minimum recommended server configuration for SEP (need clear proof/reference document from Symantec)
--> With every release Symantec will provide system requirements document, you should check the same.
for an e.g. check this article
http://www.symantec.com/docs/TECH165172
Support matrix (with detail workflow diagram mentioning activity escalation flow to Symantec)
--> I think only business partner can provide you this info.