OK, so given that you already have the electronics and code working and performing exactly the task you want, then at this moment you already have the Arduino Micro connected with a cable using a micro USB plug.
Your question then is - how to remove the socket from the Arduino Micro, cut the plug off the cable and wire the cable directly to the pads on the Arduino Micro PCB itself.
This is certainly do-able, the links Simpson_Jr has given you (including the sub-link for the Micro-USB connector pinout) detail the standard wire colours in order to match the pins on the Micro-USB connector where it was mounted on the board. It would however, require you to desolder the SMD Micro-USB socket from the board which requires considerable skill and similarly, solder the wires in its place. Having done so (and verified success), I would advise you to tie the cable securely to one of the adjacent corner holes in the Arduino Micro PCB and encapsulate your new connections and the end of the cable in a blob of epoxy, never to be altered.
All in all, a very difficult job.