I have installed production ArcGIS Server systems over a dozen times (rough estimate not counting upgrades) at different locations and under different IT environments. It is a world of change from the old ArcIMS days and so much easier. No Apache Server, no Tomcat, no enabling user permissions to make changes to the environmental variables or setting the %JAVA_HOME variable (How many times did a Java update break our sites? Ugh!). That being said each install has its own idiosyncrasies and challenges...