It looks like the F# project templates are using a path to an older version of F#. There is a discussion about this on the GitHub repository for the F# addin. Hopefully the project template can be updated to support different versions of F# being installed. For now you can modify your project file.
MSBuildExtensionsPath32 points to C:\Program Files (x86)\MSBuild
So you could try modifying the project template to use the following path, which should work on your machine:
<Import Project="$(MSBuildExtensionsPath32)\..\Microsoft SDKs\F#\3.1\Framework\v4.0\Microsoft.FSharp.Targets" />