I ended up calling for technical support. I installed IIS on my arcgis server, then the web adaptor and had problems. It turns out I was using the wrong account. I needed to be using the ArcGIS server manager account. That worked for my ArcGIS server, but not for our web server. My ArcGIS Server is Windows 2008 R2, IIS 7. Our web server is Windows 2003, IIS 6.0. That is not working and technical support has not gotten back to us on their results. They were going to test out our 2003 configuration.
I'll post what I find out from ESRI.