I know that in Safari if you want to change a keyboard shortcut you just set an application specific rule in keyboard settings under system preferences with the exact name of the menu item you want to change and your desired shortcut. My problem is, I have a specific function (Language Preferences > Select the previous/next input source in the Input menu) associated with the keyboard shortcuts cmd-1 and cmd-2 and Safari has these set default to go to bookmarks 1 and 2 in the bookmarks menu. I tried setting a specific keyboard shortcut for Safari and assigning cmd-1 and cmd-2 to the function I desire yet it still jumps to the bookmarks in the browser when I try it. I would be glad to just remove the default behavior of cmd-1-9 for bookmarks menu shortcuts in Safari and have Safari not use them at ALL but I see no way to do so. In Firefox my cmd-1 and cmd-2 work just fine since Firefox has nothing else set to use them. I also tried setting the first two bookmarks to nil in Terminal and yet although the cmd-1 no longer appeared next to them in the bookmarks menu the default behavior of jumping to them on those key presses DID. Very bizarre.... In respect to keyboard shortcuts I must say I wish Safari was a bit more easily and intuitively configurable.