After trying to solve the code for multiple weeks, we changed the wiring as well, however that did not work but we have finally fixed the code so here it is, and the v2 gun is almost finished as well so here's the code: 

#include <Mouse.h>
#include "Keyboard.h"

int horzPin = A0;  // Analog pin for horizontal joystick
int vertPin = A1;  // Analog pin for vertical joystick
int selPin = 8;    // Joystick button (select pin)

int vertZero, horzZero;   // Stores joystick center values
int vertValue, horzValue; // Stores joystick axis readings
const float sensitivity = 200.0; // Sensitivity (float for precision)
int mouseClickFlag = 0;

int invertMouse = -1; // Non-inverted movement

// Button pin assignments
const int buttonW = 2;  // Button for printing 'W'
const int buttonS = 3; // Button for printing 'S'
const int buttonMouseClick = 4; // Button for mouse left click

void setup() {
  // Joystick setup
  pinMode(horzPin, INPUT);
  pinMode(vertPin, INPUT);
  pinMode(selPin, INPUT_PULLUP);
  vertZero = analogRead(vertPin); // Calibrate initial neutral position
  horzZero = analogRead(horzPin);
    Mouse.begin();    // Initialize mouse emulation
  Keyboard.begin(); // Initialize keyboard emulation

  // Button setup
  pinMode(buttonW, INPUT_PULLUP); // Button for 'W'
  pinMode(buttonS, INPUT_PULLUP); // Button for 'S'
  pinMode(buttonMouseClick, INPUT_PULLUP); // Button for mouse left click
}

void loop() {
  // --- Joystick Movement ---
  vertValue = analogRead(vertPin) - vertZero; // Vertical movement
  horzValue = analogRead(horzPin) - horzZero; // Horizontal movement
    if (abs(vertValue) > 5) { // Ignore small offsets
    Mouse.move(0, vertValue / sensitivity); // Move mouse vertically
  }
  if (abs(horzValue) > 5) { // Ignore small offsets
    Mouse.move(invertMouse * horzValue / sensitivity, 0); // Move mouse horizontally
  }

  // --- Joystick Button (Print 'R') ---
  if (digitalRead(selPin) == LOW) {     Keyboard.print("R"); // Print 'R' when joystick button is pressed
    delay(50); // Debounce delay
  }

  // --- Button 1: Print 'W' Continuously ---
  if (digitalRead(buttonW) == LOW) {     Keyboard.print("W"); // Print 'W' while button is held
    delay(50); // Typing rate
  }

  // --- Button 2: Print 'S' Continuously ---
  if (digitalRead(buttonS) == LOW) {     Keyboard.print("S"); // Print 'S' while button is held
    delay(50); // Typing rate
  }

  // --- Button 3: Simulate Left Mouse Click ---
  if (digitalRead(buttonMouseClick) == LOW) {     Mouse.click(MOUSE_LEFT); // Perform a mouse left click
    delay(50); // Avoid multiple rapid clicks
  }
}