Solution :
I have gone through your question and I understood it.
I had faced the similar issue in the past and so know the solution on it.
The <fastCGI> settings must be done in your applicationHost.config file (in your system.webServer section) of IIS. Just putting it into your web.config does not work (I can confirm it by testing it on a local IIS). An example of the configuration may look like as below :
<fastCgi>
<application
fullPath="C:\home\Python27\python.exe"
arguments="C:\home\Python27\wfastcgi.py"
maxInstances="16"
idleTimeout="21600"
instanceMaxRequests="10000000"
signalBeforeTerminateSeconds="60"
xdt:Transform="InsertIfMissing"
xdt:Locator="Match(fullPath)">
<environmentVariables>
<environmentVariable name="PYTHONHOME" value="C:\home\Python27" />
</environmentVariables>
</application>
</fastCgi>
You must adjust your configuration according to above configuration.
This should help you in solving it for a local IIS where you can edit the applicationHost.config.
Further Readings :
You can find more hints below:
https://github.com/Azure/azure-python-siteextensions/issues/2.