Hello Tracy, You could have Portal install on the Web Adaptor machine or on it own machine, it all depends on what you are trying to accomplish, security policies and who will be using Portal. But to be able to use the Web Adaptor full security purpose, I would remember install the Web Adaptor on a Web Server machine and Portal on a different machine. One thing to remember is that you will not be able to use one Web Adaptor to configure both ArcGIS Server and Portal. What this mean is that you will only be able to configure one Web Adaptor to one application site, you should install one Web Adaptor for ArcGIS Server and one Web Adaptor for Portal. As for your 10.3.1 question, there shouldn't be any reason to not upgrade to 10.3.1 beside needing to upgrade people's desktop or maybe compatibility with other third party application you may have within your environment. I hope this help answers your questions.
... View more