Well, let's get the easy one out of the way 1st 
Licensing of the runtime. The runtime is free for win apps. For web apps it is also free - as long as the app is used within your organization. If the web app is used external to your org, you do need to obtain additional licensing. And for that you will have to contact sales: 866-681-3435
Now, the actual issue:
Normally, the runtime is deployed using the MSI, MSM or CLickOnce, Nothing wrong with you installing VS on the server and then CR, but I suspect you're using up a VS license for that (expensive(?)), but that is a decision for you to make. E.g.; uninstalling VS and running the CR SP 9 MSI should suffice. To actually get the viewer working, I'd like you configure the viewer as per the direction in this blog:
- Ludek