1) I've just extracted the notification library from Guard into: https://github.com/guard/notiffany
(so all future notifications issues like this one should be reported there from now on).
4) There may be other notifies, e.g. I like xosd (It's not as pretty, but the features are great) - I might be worth adding support for it in the Notiffany project
Also, there used to be a "hacked" libnotify PPA - but it was no longer maintained (and it stopped working with Ubuntu 12 I think) - you might want to get the sources, fix the timeout and install it locally.
That's all the ideas/suggestions I have - sorry.