thaddeus, I updated my documentation at http://catdancer.github.com/mz.html to give an explanation of the patch command and how to use it. Take a look and let me know if it's helpful. (Note github has come kind of caching bug with their pages so if you go back to the page your browser will display the old version of the page if it has a copy of it in its cache; you must click the refresh button or press F5 to see the new version).
I also crossed out the explanation of how to apply the patch using "git pull", since as you discovered "git pull" doesn't work if the two git repositories don't share a common ancestor. (I suspect there is a way to do this using git, but I'll have to go looking for it).
