@Jonathan_Ashmore: any chance you could post the contents of configure.log produced when the script fails to find Eigen3? Just so we can figure out how to fix it properly.
Also, would you mind checking whether you have pkg-config installed and in your PATH? If not, try installing it and invoke ./configure again, see if that helps at all. I think the procedure would be:
$ brew install pkg-config
That should allow ./configure to query the correct settings for Eigen3…