Which files would I have to keep to make sure all settings work as before?
amule.conf of course but anything else?
I suggest to keep all your preferences that are stored under your user's folder:
~/Library/Application Support/aMule
If you want know their meaning, search in the wiki.
If you run SVN version maybe you have to reconfigure some aesthetic settings.
I also suppose that some of the other components that you suggest are optional to copy might be updated in the future so it might then be important to copy everything.
Copy only what you need (often only aMule).
If you want to use aMuleGUI, you should use the same version of aMule (amule/amuled).
aMule.app already contains several command line utilities and the daemon version of amule.
EDIT:
See here:
http://www.amule.org/wiki/index.php/AMule_filesand here:
http://www.amule.org/wiki/index.php/FAQ_utils