I want to get around the 401 authentication error and get a 200 http status. I am not sure how to set the inputs.conf file to support this when the website uses windows authentication.
The Website Monitoring app tries to detect the type of authentication automatically. It is possible this isn't working properly.
Can you check the following logs and see if the inputs appear to be using NTLM authentication?
index=_internal sourcetype="web_availability_modular_input" auth_type
Lots of these
2017-02-21 20:36:52,423 DEBUG Discovered auth_type=ntlm
Ok, so it is using ntlm which is what it should be using. Are there any other logs that indicate why this may be failing (look for any errors too)? You may want to look at logs on the Windows device to see if provides some insight.