Amr,
This sounds like you may have permission issues in the folder you .svc is running from, please can you check and see if the following permissions are there:
- \IIS_IUSERS
- \IIS_IUSR —If running webservice in Anonymous Mode
For the issue with protocol Mapping, please ensure that the app Pool you are using for the IIS site is setup to use .net 4, as from what I understand protocol mapping is only available in .net 4.
Hope this helps