We have three separate instances of Windchill PDMLink 9.1 M070 which have databases migrated from Oracle to MSSQL 2008R2. Running fine without any issues.
We actually migrated Windchill 9.1 M060 database from oracle to MSSQL 2005, which was disaster as in M060 was missing required database table instances and we ended up with performances issues.
So we first upgraded from MSSQL 2005 to MSSQL 2008 R2. And searched out to find missing indexes. (I can tell you the process) After applying missing indexes problems resolved.
Later when we updated from Windchill 9.1 M060 to Windchill 9.1 M070, we found most of the indexes were there in M070.
Again there are guidelines available in PTC site about configuring MSSQL server for best performance.