X_UPの例ですが、X_DN、Y_UP、_Y_DN、Z_UP、Z_DNも同様に変更します。

変更前
  if (X_UP == LOW) { // X-axis Right
    Keyboard.press(KEY_RIGHT_ARROW);
    delay(300);//delay(100～300)
    Keyboard.release(KEY_RIGHT_ARROW);
    delay(1);
  }

変更後
  if (X_UP == LOW) { // X-axis Right
    Keyboard.press(KEY_RIGHT_ARROW);
  }

#include "Keyboard.h"
/* Arduino pro microのピン配置とKeySwitchの配置を最短結線を優先した為、
 KeySwitch名とピン番号がランダムになりました。*/
int TAB = 10;
int SHIFT = 16;
int Cycle_Start = 15;
int Reset = 20;
int Jog_Mode = 14;
int Cycle_Jog_Step = 6;
int Slow_Jog_UP =5;
int Slow_Jog_DN = 4;
int Zero_X = 9;
int Zero_Y = 8;
int Zero_Z = 7;
int X_UP = 2;
int X_DN = 19;
int Y_UP = 3;
int Y_DN = 21;
int Z_UP = 1;
int Z_DN = 0;
int STOP = 18;

void setup() {
  Keyboard.begin();
  pinMode(TAB, INPUT_PULLUP);
  pinMode(SHIFT, INPUT_PULLUP);
  pinMode(Cycle_Start, INPUT_PULLUP);
  pinMode(Reset, INPUT_PULLUP);
  pinMode(Jog_Mode, INPUT_PULLUP);
  pinMode(Cycle_Jog_Step, INPUT_PULLUP);
  pinMode(Slow_Jog_UP, INPUT_PULLUP);
  pinMode(Slow_Jog_DN, INPUT_PULLUP);
  pinMode(Zero_X, INPUT_PULLUP);
  pinMode(Zero_Y, INPUT_PULLUP);
  pinMode(Zero_Z, INPUT_PULLUP);
  pinMode(X_UP, INPUT_PULLUP);
  pinMode(X_DN, INPUT_PULLUP);
  pinMode(Y_UP, INPUT_PULLUP);
  pinMode(Y_DN, INPUT_PULLUP);
  pinMode(Z_UP, INPUT_PULLUP);
  pinMode(Z_DN, INPUT_PULLUP);
  pinMode(STOP, INPUT_PULLUP);
}

void loop() {
  TAB = digitalRead(10);
  SHIFT = digitalRead(16);
  Cycle_Start = digitalRead(15);
  Reset = digitalRead(20);
  Jog_Mode = digitalRead(14);
  Cycle_Jog_Step = digitalRead(6);
  Slow_Jog_UP = digitalRead(5);
  Slow_Jog_DN = digitalRead(4);
  Zero_X = digitalRead(9);
  Zero_Y = digitalRead(8);
  Zero_Z = digitalRead(7);
  X_UP = digitalRead(2);
  X_DN = digitalRead(19);
  Y_UP = digitalRead(3);
  Y_DN = digitalRead(21);
  Z_UP = digitalRead(1);
  Z_DN = digitalRead(0);
  STOP = digitalRead(18);

  if (TAB == LOW) { // TAB-KEY
    (KEY_TAB);
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Cycle_Start == LOW) {  // Cycle_Start
    Keyboard.press(KEY_LEFT_ALT);
    Keyboard.press('r');
    delay(100);
    Keyboard.releaseAll();
    delay(100);
  }
  if (Reset == LOW) {  // RESET
    Keyboard.press('[');//何故か'['入力で'@'を出力（@が目的なのに文字化け）
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Cycle_Jog_Step == LOW) {  // Cycle_Jog_Step/Velocity
    if (SHIFT == LOW) {  // Step/Velocity:OEM=304,Hotkey=34900
      Keyboard.press(KEY_LEFT_CTRL);
      Keyboard.press(KEY_LEFT_ALT);      
    }
    else {  // Cycle_Jog_Step:OEM=171,Hotkey=2132
      Keyboard.press(KEY_LEFT_ALT);
    }
    Keyboard.press('t');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Jog_Mode == LOW) {  // Jog_Mode/Velocity Onry
    if (SHIFT == LOW) {  // Velocity Onry:OEM=303,Hotkey=34893
      Keyboard.press(KEY_LEFT_CTRL);
      Keyboard.press(KEY_LEFT_ALT);
    }
    else {  // Jog Mode:OEM=245,Hotkey=2125
      Keyboard.press(KEY_LEFT_ALT);
    }
    Keyboard.press('m');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Slow_Jog_UP == LOW) {  // Slow_Jog_UP/Single Step
    if (SHIFT == LOW) {  // Single Step:OEM=305,Hotkey=34901
      Keyboard.press(KEY_LEFT_CTRL);
      Keyboard.press(KEY_LEFT_ALT);
    }
    else {  // Slow_Jog_UP:OEM=111,Hotkey=2133
      Keyboard.press(KEY_LEFT_ALT);
    }
    Keyboard.press('u');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Slow_Jog_DN == LOW) {
    if (SHIFT == LOW) {  // Slow_Jog_UP:OEM=306,Hotkey=34884
      Keyboard.press(KEY_LEFT_CTRL);
      Keyboard.press(KEY_LEFT_ALT);
    }
    else {  // Slow_Jog_UP:OEM=112,Hotkey=2116
      Keyboard.press(KEY_LEFT_ALT);
    }
    Keyboard.press('d');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Zero_X == LOW) { // Select X-axis for MPG 1/Zero-X-axis
    if (SHIFT == LOW) { // Zero_X-axis 
      Keyboard.press(KEY_LEFT_ALT);
    }
    else { // Select X-axis for MPG 1
      Keyboard.press(KEY_LEFT_ALT);
      Keyboard.press(KEY_LEFT_CTRL);
    }
    Keyboard.press('x');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Zero_Y == LOW) { // Select Y-axis for MPG 1/Zero_Y-axis
    if (SHIFT == LOW) { // Zero_Y-axis
      Keyboard.press(KEY_LEFT_ALT);
    }
    else { // Select Y-axis for MPG 1
      Keyboard.press(KEY_LEFT_ALT);
      Keyboard.press(KEY_LEFT_CTRL);
    }
    Keyboard.press('y');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (Zero_Z == LOW) { // Select Z-axis for MPG 1/Zero_Z-axis
    if (SHIFT == LOW) { // Zero_Z-axis
      Keyboard.press(KEY_LEFT_ALT);
    }
    else { // Select Z-axis for MPG 1
      Keyboard.press(KEY_LEFT_ALT);
      Keyboard.press(KEY_LEFT_CTRL);
    }
    Keyboard.press('z');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
  if (X_UP == LOW) { // X-axis Right
    Keyboard.press(KEY_RIGHT_ARROW);
    delay(300);//delay(100～300)
    Keyboard.release(KEY_RIGHT_ARROW);
    delay(1);
  }
  if (X_DN == LOW) { // X-axis Left
    Keyboard.press(KEY_LEFT_ARROW);
    delay(300);//delay(100～300)
    Keyboard.release(KEY_LEFT_ARROW);
    delay(1);
  }
  if (Y_UP == LOW) { // Y-axis Forward
    Keyboard.press(KEY_UP_ARROW);
    delay(300);//delay(100～300)
    Keyboard.release(KEY_UP_ARROW);
    delay(1);
  }
  if (Y_DN == LOW) { // Y-axis BackForward
    Keyboard.press(KEY_DOWN_ARROW);
    delay(300);//delay(100～300)
    Keyboard.release(KEY_DOWN_ARROW);
    delay(1);
  }
  if (Z_UP == LOW) { // Z-axis UP
    Keyboard.press(KEY_PAGE_UP);
    delay(300);//delay(100～300)
    Keyboard.release(KEY_PAGE_UP);
    delay(1);
  }
  if (Z_DN == LOW) { // Z-axis Down/Probe
    if (SHIFT == LOW) { // Probe to Z-axis :OEM=707,Hotkey=32847
      Keyboard.press(KEY_LEFT_CTRL);    
      Keyboard.press('o');
    }
    else { // Probe to Z-axis
    Keyboard.press(KEY_PAGE_DOWN);
    }
    delay(300);
    Keyboard.releaseAll();
    delay(1);
  }
  if (STOP == LOW) { // STOP/ Goto Zero
    if (SHIFT == LOW) { // Goto Zero
      Keyboard.press(KEY_LEFT_CTRL);
      Keyboard.press(KEY_LEFT_ALT);
    }
    else { // STOP
      Keyboard.press(KEY_LEFT_ALT);
    }
    Keyboard.press('s');
    delay(100);
    Keyboard.releaseAll();
    delay(200);
  }
}