All other things being equal, use the Pat-5 in the best physical condition. Some parts are recycled, including the pushbutton switches, tone controls, selector switch, and jacks (unless you add the jack set kit option). If both Pat-5s are working now, check them out for good signal continuity on all the jacks and switch functions. A major switching dropout in the main bank of pushbutton switches is a real pain in the ass to deal with after the fact.
It does not matter which version of the Pat-5 you use from a circuit standpoint, the audio circuits are replaced, the important things are the condition of the necessary recycled hardware.
Frank Van Alstine