The configuration file is located at "C:\ProgramData\QlikTech\QvWebServer\config.xml" (Win 2008, Windows 7) or "C:\Documents and Settings\All Users\Application Data\QlikTech\QvWebServer\config.xml" (Windows 2003). Most settings can be changed using the Management Console http://localhost:4780/qemc
It is easiest to configure the SSL certificate using the IIS Wizards. Amend the SSL Port in QlikView Web Server from -1 to 443. Observe the startup in the QvWS logs. I recommend starting the Windows "Net TCP Port Sharing" service too.
Otherwise contact Support email@example.com