Branch rev5 of project A's folder into a folder in your project's folder, branch rev3 of project B's folder into a folder in your project's folder. Get your project to refer to its own copy, rather than the shared copies you branch from. (This isn't quite like git submodules, but that's probably the closest thing git has.)
You do the usual 3-way merge thing to push your changes upstream, or pull upstream changes into your copy. As with git, the VCS tracks which revision of upstream your copy is up to date with, which is how it determines the base for the 3-way merge.
