So one thing that has come up a lot, is how do I re-index all of the tables in my backend FIMSynchronizationService Database. I have compiled this document together to help understand how to accomplish this task.
How to re-index all of the tables in the backend FIMSynchronizationService Database: http://social.technet.microsoft.com/wiki/contents/articles/how-to-reindex-all-of-the-tables-in-the-backend-fimsynchronizationservice-database.aspx
Note, that this script will work for MIIS 2003 and ILM as well. The database name is different, but it will still work.