Regarding the SSL certificate, there is not a unique certificate for IIS or Tomcat. They are all the same. Does https work for you when you use a self-signed certificate instead of importing one?
I have found that there IS a difference. I was using GoDaddy as my CA, and when you download the certificate, it asks your where you intend to use it. I was choosing IIS7. ArcGIS for Server would not import the intermediate certificate, and security could not be enabled. On the advice of Esri tech suppport, I chose "other" and proceded without trouble.
I was running into this same issue myself. I'm running 10.1 SP1 and was able to successfully implement this workflow using an existing CA cert. The setup was extremely sensitive and would only work for me when done in the following sequence.1)Install CA cert. on IIS2)Enable https and http in AGS Admin.3)Restart Server (this is key)4)Log back into AGS Admin. Choose and save settings *again for the "self signed" cert. (the default one)5)Run web adapter with the "https://xyz:6443/arcgis/admin" for admin dir.These items in this specific order were the only way I successfully implemented using SSL with an existing CA certificate while maintaining http & https access. It was a lot of trial and error to make this work. Hope this helps some of you out there.
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