Glad to hear updating XCode was all it took.
As to the Eigen3 issue, can you try installing the pkg-config package via macports/homebrew (along with the Eigen3 one), and trying again? I’m not sure that’s what the problem is (see this post, where the same issue is cropping up), but I have a feeling that might fix it. If it does, you won’t need the standalone download or setting the EIGEN_CFLAGS, it should just work.
Clearly, it none of that works, we’ll need to reassess. In that case, I’ll ask you to post your configure.log output again - that’s the only way we’re going to have any hints as to what the issue might be.