We ran into this error when deploying a solution from the build server:

Could not load file or assembly 'System.Web.Http.WebHost, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)

Since this was a new web server and this solution used Nuget (and Nuget Package Restore) for Web Api, we assumed the Nuget packages needed to be updated but whatever type of updating we tried, we were unable to resolve the issue on the deployed web server.  After all sorts of checking and confirming of installed packages and assemblies, we just deleted the packages folder on the build server (the one created by Nuget Package Restore):

And then a fresh build solved the problem!

We are not exactly sure what happened here but most likely Nuget Package Restore had pulled down a newer version of the System.Web.Http.WebHost assembly that was not compatible with our project.  But we are not exactly sure why the Visual Studio project (MSBuild) kept trying to use the newer version instead of the proper version for the project reference.  This project had been upgraded to .NET Framework 4.5 several weeks ago and then rolled back to .NET Framework 4.0 because of a different issue.  This could explain where the incorrect version of System.Web.Http.WebHost came from but why Nuget Package Restore kept the wrong one is unknown and why the project kept building with the incorrect assembly is unknown too. 

In any case, for anyone that runs into the same issue, delete your packages folder and let Nuget Package Restore pull a fresh set of assemblies.

Full Exception information:
    Exception type: HttpException
    Exception message: Could not load file or assembly 'System.Web.Http.WebHost, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
   at System.Web.HttpApplicationFactory.EnsureAppStartCalledForIntegratedMode(HttpContext context, HttpApplication app)
   at System.Web.HttpApplication.RegisterEventSubscriptionsWithIIS(IntPtr appContext, HttpContext context, MethodInfo[] handlers)
   at System.Web.HttpApplication.InitSpecial(HttpApplicationState state, MethodInfo[] handlers, IntPtr appContext, HttpContext context)
   at System.Web.HttpApplicationFactory.GetSpecialApplicationInstance(IntPtr appContext, HttpContext context)
   at System.Web.Hosting.PipelineRuntime.InitializeApplication(IntPtr appContext)

Could not load file or assembly 'System.Web.Http.WebHost, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)
   at Global.Application_Start(Object sender, EventArgs e)

Did you know that you can install MSBuild to your build and deployment server individually without needing to install Visual Studio?

You can get MSBuild 12 – aka Microsoft Build Tools 2013 – from http://www.microsoft.com/en-us/download/details.aspx?id=40760.

Downloading and installing will give you MSBuild.exe in C:\Program Files (x86)\MSBuild\12.0\Bin

The 64-bit version is located in C:\Program Files (x86)\MSBuild\12.0\Bin\amd64.

Setting up a build server on a new install of Windows Server 2012 R2 and ran into the following warning when building the projects:

Warning MSB3644 - The reference assemblies for framework ".NETFramework,Version=v4.5" were not found. To resolve this, install the SDK or Targeting Pack for this framework version or retarget your application to a version of the framework for which you have the SDK or Targeting Pack installed. Note that assemblies will be resolved from the Global Assembly Cache (GAC) and will be used in place of reference assemblies. Therefore your assembly may not be correctly targeted for the framework you intend.

The build server was a fresh machine and the issue was Visual Studio 2013 needing to be installed on the server.  Installing Visual Studio Professional 2013 without any options resolved the issue.

• Under optional Features uncheck all the options to speed up the install.
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