I have a PNP, center positive DC jack effect that I'd like to add an LED to. I am following the true bypass wiring layout at GeneralGuitarGadgets except switching the polarity. Can I simply add the LED and only switch the direction of the LED and resistor? Any problems? Is it this simple or am I missing something?

it will work - like you said, all you need to do is to make sure the LED is connected (through a resistor) from +9V to ground (take your pick *where* you hook it up) and that it's pointing the right way.
Good luck!