Ah, now I see.
You want to make an arcade-style controller with 4 buttons and a joystick that plugs in via USB. Amiright?
There are several ways to approach this.
Hacking a NES controller and connecting it through the retroport is a lot more work than using something like Vigo's
ZD Encoder (gamepad-style encoder) or the AVR Encoder by Degenatrons. (keyboard-style encoder) The added bonus to using these other encoders is that you have room to expand/grow. What if you decide you want to play SNES games, too? With the NES hack, you have no room to grow like you have with the others.
With all that in mind, Slagcoin has all the info you are asking for
here including this diagram of where to solder your signal and ground wires. (other controller board diagram links listed 2/3rds of the way down under "PCB Diagrams")

The signal traces -- blue circles above -- connect to the corresponding Normally Open (NO) switch contact. The joystick will appear backwards since pushing up closes the switch closest to you and pushing right closes the switch on your left.
The ground "daisy-chain" connects all the Common (Com) switch terminals to the trace with the red circle above.

Image credit: RandyT from Groovy Game Gear.

Scott