Hi Henrychan,
There are a number of ways to improve DTM performance.
You can use command prompt to run the DTM job.
To know more about running DTM jobs through command prompt, see this post:
http://community.imanami.com/forums/thread/679.aspx
You can also remove log files of previously run jobs that may be slowing down DTM.
I don't believe the EmployeeNumber attribute in AD is indexed. You can update the EmployeeNumber attribute in Active Directory so that it is indexed (details on how to do this can be found on the Microsoft web site).