Server 2003 R2 Can Not be used in the Workgroup Form so it has to be set as a Domain and you'll need at least 1 X 5 Pack of CAL's or Terminal Service Licenses.
If they are using the Small Business Server 2003 R2 this comes with Exchange, ISA and some other things that you may not need but you'll need both Exchange and ISA and be able to configure them to prevent intrusions. Then because they will be running a Domain you'll need to transfer all the Workgroup Machines over to the Domain.
If you haven't done this previously and you don't know the current Network I would really suggest that you make a Long Weekend Available I spent 3 days changing from 2003 SBS Server to 2003 R2 Server with SQL 2005. It only took a couple of hours to setup the server and then the best part of the remaining 3 days to work out what had been done by the previous person who setup the system. That was a real pain and time consuming as well. Of course after I found things the guy who owned the place said Oh Yes I did that but when asked insisted that there where no changes to the original configuration. So it was a slow and painful exercise.
As to what you charge that depends on the time taken and how much you wish to keep this place as a customer it may be worthwhile to not charge for all the time that you spend there and keep a customer rather than get a lot on money up front and never see that customer again. You'll also need to see what others in the area are charging and work from that.
Col
