I may just be thinking about this problem the wrong way and missing an obvious solution.
I have multiple copies of the same files in several places on my computer that I edit via Sourcetree, Visual Studio and Notepad++. All of these files are from the same module built into different projects, and I often find myself having to use winmerge to recombine them after changes are made to the same file in two separate locations. Is there any tool or method I can use to keep all the files in sync or make them reference one another?
Make them all hardlinks: one file on disk, many references wherever you want.
Source control software maintain links to share a file between several projects. If you make changes in one project, changes will be automatically propagated to other projects.
Sinne you are using VisualStudio, please check whether your license covers Microsoft SourceSafe which is a easy to use source Control software. Otherwise take a look on open source products such as SVN.