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This error suggests that you've configured the web application to run as an ASP.NET 2.0 application, instead of an ASP.NET 4.0 application. You'll need to go back to the Internet Information Services (IIS) manager and change the Continua's application pool to target the .NET 4.0.
My Remote Agent
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does not have access to the server via UNC or SSH
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This error occurs when the agent can communicate with server but the server cannot communicate with the agent. The only time an agent talks to the server is to register itself to tell that server that it is still online. All other communication originates from the server and the server tells the agent to do things.
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