With the following simple entity class, EF4.1 Code-First will create Clustered Index for the PK UserId
column when intializing the database.
You don't need to predict name of auto generated index. You just need to select name of the index. For SQL server you can use query like:
SELECT I.Name
FROM sys.indexes AS I
INNER JOIN sys.tables AS T ON
I.object_Id = T.object_Id
WHERE I.is_primary_key = 1
AND T.Name = 'Users'
Once you get the name in your custom initializer you can alter old index and create a new one.