You can bind to whatever keys you like, of course, but may I suggest using the same ⌘R combo that's used to invoke the command in the regular bundle? If you plan to use your modified command exclusively you can just delete the original's keystroke. If you plan to use both commands in different circumstances it's okay to have them both bound to the same key. When there's a conflict like this (multiple commands bound to the same keystroke, all valid in the current scope) it pops up a menu of choices. You can select the one you want by number. So, ⌘R1 would invoke the original command, ⌘R2 would invoke the modified version.
As an example, try ⌃⇧A (ctrl-shift-A). That key is used as a catch-all by a lot of bundles. Assuming you have any of those installed you should see the pop-up with a bunch of choices.