Matt, Dave M.: We definitely agree - unfortunately, fighting on this front has just gotten to be too difficult. Perhaps Apple will make them not suck in the future - we can hope.

Greg C: SoundSource 2.5 should remove everything from older versions from the menu bar when you run it. Just open it and enjoy - you'll be all set!

However, if you're concerned about removing the old (inert) files, you can do that manually. Those can be found here:

/Library/Bundles/SoundSource.menu
or
~/Library/Bundles/SoundSource.menu
and
/Library/InputManagers/Menu Extra Enabler

Just delete those, and they'll be gone. But even if you don't, they're inert (like old prefs files, say), and won't affect anything.