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On a related note, does anyone here have a link to an ESRI article which describes the position of ArcGIS Server with regards to support of the 4.0/4.5 framework?
There is such an article for Desktop/Engine.
I'd leave the web adaptor alone, i.e. run it as ESRI configures it.
I wish that ESRI posted a clear postion statement on the 4.0/4.5 framework but I cannot find it.
We definitely use the later frameworks but leave the web adaptor untouched.
The only value I can see in running it with the 4.0 framework is that you might be able to avoid having to install 2.0/3.5 on the server. I just installed ArcGIS Server 10.1 SP1 on Windows Server 2012 and had to install 2.0/3.5 because ArcGIS Server required it.