Replace serial monitor input with matrix keypad

try something like this (typed here based on your code, so mind typos and possible errors). This should give you an idea how you could structure the code. (note I changed the baud rate for the Serial monitor to 115200, adjust your console)

#include <Keypad.h>
#include <AccelStepper.h>
#include <LiquidCrystal_I2C.h>

LiquidCrystal_I2C lcd(0x27, 16, 2); // set the LCD address to 0x27 for a 16 chars and 2 line display
AccelStepper stepperX(1, 12, 11);   // 1 = Easy Driver interface

const byte home_switch =  10;

// Stepper Travel Variables
long TravelX;  // Used to store the X value preovided by the user


//keypad setup
const int ROW_NUM = 4; //four rows
const int COLUMN_NUM = 4; //four columns

char keys[ROW_NUM][COLUMN_NUM] = {
  {'1', '2', '3', 'A'},
  {'4', '5', '6', 'B'},
  {'7', '8', '9', 'C'},
  {'*', '0', '#', 'D'}
};

byte pin_rows[ROW_NUM]      = {5, 4, 3, 2}; //connect to the row pinouts of the keypad
byte pin_column[COLUMN_NUM] = {9, 8, 7, 6}; //connect to the column pinouts of the keypad

Keypad keypad = Keypad( makeKeymap(keys), pin_rows, pin_column, ROW_NUM, COLUMN_NUM );

String keypadInput;

void lcdEnterValue() {
  lcd.clear();
  lcd.print(F("enter value:"));
  lcd.setCursor(0, 1);
  Serial.println(F("Enter Travel distance (Positive for CW / Negative for CCW and Zero for back to Home): "));
}


bool readKeypad(long& newDestination) {
  long userInput = 0;
  char key = keypad.getKey();
  if (key) {
    if (key >= '0' && key <= '9') {     // only act on numeric keys ==> HOW DO YOU ENTER NEGATIVE VALUES?
      keypadInput += key;               // append new character to input string
      lcd.print(key);
    } else if (key == '#') {
      if (keypadInput.length() > 0) {
        userInput = keypadInput.toInt();
        keypadInput = "";               // clear input

        if (userInput < 0 || userInput > 140250) {  // Make sure the position entered is not beyond the HOME or MAX position
          Serial.println(F("\nPlease enter a value greater than zero and smaller or equal to 70250.....\n"));
          lcd.clear();
          lcd.print(F("invalid value."));
          delay(3000);
          lcdEnterValue();
          return false;
        } else {
          lcd.clear();
          lcd.setCursor(0, 0);
          lcd.print(F("Moving to:"));
          lcd.print(userInput);
          Serial.print(F("Moving stepper into position: "));
          Serial.println(userInput);
          delay(1000);  // Wait 1 seconds before moving the Stepper
          newDestination = userInput;
          return true;
        }
      }
    }
  }
  return false;
}

void homing() {
  //  Set Max Speed and Acceleration of each Steppers at startup for homing
  stepperX.setMaxSpeed(800.0);      // Set Max Speed of Stepper (Slower to get better accuracy)
  stepperX.setAcceleration(800.0);  // Set Acceleration of Stepper

  // Start Homing procedure of Stepper Motor at startup
  lcd.setCursor(0, 0);
  lcd.print(F("HOMING"));
  Serial.print(F("Stepper is Homing"));

  long initial_homing = -1; // Used to Home Stepper at startup

  while (digitalRead(home_switch) == HIGH) {
    stepperX.moveTo(initial_homing);  // Set the position to move to
    initial_homing--;  // Decrease by 1 for next move if needed
    stepperX.run();  // Start moving the stepper
    delay(1);
  }

  stepperX.setCurrentPosition(0);   // Set the current position as zero for now
  stepperX.setMaxSpeed(100.0);      // Set Max Speed of Stepper (Slower to get better accuracy)
  stepperX.setAcceleration(100.0);  // Set Acceleration of Stepper
  initial_homing = 1;
  delay(15);                        // anti-bounce

  while (digitalRead(home_switch) == LOW) {
    stepperX.moveTo(initial_homing);
    initial_homing++;
    stepperX.run();
    delay(1);
  }

  stepperX.setCurrentPosition(0);

  lcd.clear();
  lcd.print(F("HOMING OK"));
  Serial.println(F("Homing OK\n"));

}

void setup() {
  pinMode(home_switch, INPUT_PULLUP);
  Serial.begin(115200);     // don't go slow.

  keypadInput.reserve(10);  // avoid dynamic allocation
  keypadInput == "";        // empty the String

  lcd.init();               // initialize the lcd
  lcd.clear();
  lcd.backlight();

  homing();

  stepperX.setMaxSpeed(1000.0);      // Set Max Speed of Stepper (Faster for regular movements)
  stepperX.setAcceleration(500.0);  // Set Acceleration of Stepper

  // Print out Instructions on the Serial Monitor at Start
  lcdEnterValue();
}

void loop() {

  if (readKeypad(TravelX)) stepperX.moveTo(TravelX);  // Set new moveto position of Stepper

  // Check if the Stepper has reached desired position
  if ((stepperX.distanceToGo() != 0)) {
    stepperX.run();  // Move Stepper if needed
  } else {
    lcd.clear();
    lcd.setCursor(0, 0);
    lcd.print("COMPLETED!");
    Serial.println("COMPLETED!");
    lcdEnterValue();
  }
}

the instructions say you can enter negative value but the code does not support it.