The way the installer works is it puts not the CMS and the MVC solutions in the same main directory. So your folder structure looks something like this:
-NewSite (MVC code)
We never use this structure. We always put the CMS and MVC files, including the sln files, in their own directory so we can leave them in their own code repositories.
Our structure looks like this:
I'm saying move your folders and files around so you can manage them easier long term.