Have you looked at WireGuard? It's a simpler protocol with much less overhead than IPsec, and has an in-kernel implementation on Linux (with in-kernel implementations in the works for the various BSDs). AFAIK there isn't any windows support at the moment, which may or may not be an issue for you.
i use the freeware ALLDUP if file names are consistent across copies use simple filename, if names are messed up i would recommend search method of "file content"
Check out Duplicity. I started using it a few weeks ago. Multiple backend options (S3, azure, google drive, etc.), ability to include/exclude folders, incremental backup options, gpg encryption. So far I am impressed.