Well, I kind of puzzled at the moment. Assuming the wiring on the machine is in decent condition and doesn't look like a bird nest, wires are going to their proper terminals, then I'm not sure just yet what's going on. If when you depress the foot switch, and it sends power to terminals 35-39, then the yellow wires that leave those terminals go to their respective control, and have power, I'm puzzled why nothing works. No drive, no swing, no boom lift, even the telescope, basket tilt and basket rotate which are on toggles. I've never seen a JLG loose all these functions when they have power. It's not unusual to loose one or two functions from a problem with the cable going down the boom, but all of them? Have you checked that 16/30 cable good?
Yes, the foot switch has two microswitches in it. They perform two functions, 1) start circuit enable/lockout, and 2) power up the function controls in the platform. The starter function you can only operate the starter with the foot switch up, if it's depressed it locks out the start circuit, that way when you have the foot switch depressed operating functions you can't accidentally engage the starter by pressing the start button with engine running. It sounds like your foot switch is working properly from what you've described, even though the two switches aren't in perfect sync with each other. It's desirable that they are, but not imperative as long as it's working properly.