Our OS is Windows Server 2008 R2 and our DB is SQL Server 2008 R2.
Its currently looking like the upgrade script removed some indexes from the DB that Windchill was using to assist with performance issues. We recreated the missing Indexes in the DB and that has significantly improved our performance. We are still have some issues with deadlocked methodservers but PTC is working on getting us a hotfix for it. Being told this hot fix is coming out with CPS04