I've tried to use the Preferences dialog in OS X to set custom keyboard shortcuts for CyberDuck - a few of them being:
"New Bookmark" works but "Disconnect" and "Edit Bookmark" are not working very well. In the menu the old keyboard shot disappeared but the new keyboard shotcut does not show up - and the assigned keyboard shortcut ( for example, Disconnect ) just does what it previously did - Duplicate.
At times I could get it to show up in the menu bar but the keyboard shortcut key would not actually work. I think you may have got the keyboard shortcuts to show up in the menu bar but were you actually able to use them to open the info window, and to toggle the creation of a new site? Another one I had trouble with was "disconnect" which I attempted to assign to Cmd+J
Ok - just tested again and seems like if I do make sure the existing shortcut has been replaced, then I can assign the new one. But I also have to restart the Cyberduck app to make the changes take effect.
I would just like to note that both of these things are different from the default way all other apps ( that I've seen so far ) manage keyboard shortcuts. In other apps:
You don't have to set a replacement keyboard shortcut if you assign a keyboard shortcut to a different menu item
You don't have to restart the app for keyboard changes to show up if you assign a default shortcut key a different shortcut and then assign the previously used shortcut key to a new, non-standard function.
So, it works, but it seems like Cybderduck handles keyboard shortcuts in a non-standard way which was leading me to think it was broken.