Sorry to leave you alone for so long, but I've been reading through many schematics and posts trying to figure this out. I recently came back to an old project where this could be useful to me, so I have an interest in solving this myself. The D+ and D- pins are not (easily) accessible on the Pro Micro, or any arduino. The only places to tap into the pins are on the actual USB port itself or the resistors attached to it.
So I have 3 ideas for you:
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Just attach a short USB micro wire to your pcb that you can plug into the micro. It may not be the most glamorous solution, but it should work. You would essentially be building a USB-type converter into your controller.
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Attach wires to the pins themselves. The USB terminals are incredibly small, so the 22 ohm resistors are the best attachment points. I would suggest using enameled copper wire, which is thin and salvageable from any old motors you have lying around (although larger/AC motors have much thicker wire, which won't work). If that's too challenging, you can attach one wire to one end of the D+ resistor, and the other wire to the opposite side of the D- port, or vice-versa.
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Probably too hardcore, but you could build your own custom arduino board with an atmega 32u4 chip (like the Pro Micro) and have your own pinout, with all your joystick and button peripherals built-in with the arduino.