RTC help need for programming timers for long strings

Start with this.
This program let you enter the time, day of week, etc from the Serial Monitor.

Get that working, then start checking the output to for the condiotions you are looking for.

/*
Test of RTC DS1307 via I2C.
 Counts 
 Seconds, 
 Minutes, 
 Hours, 
 Date of the Month, 
 Month, 
 Day of the week, and 
 Year with Leap-Year
 
 56 bytes battery backed RAM
 Square Wave Output, can connect to INT2/D6 or PD7
 */

/*
Modified to Run thru IDE Serial port
*/
#include <Wire.h>

//variables
byte seconds_address = 0x00;
byte seconds; // bit 7 = Clock Halt, Enabled = 0, Halt = 1
// bits 6-5-3 = tens of seconds 0-6,  bits 3-2-1-0 = units of seconds, 0-9

byte minutes_address = 0x01;
byte minutes;  // bits 6-5-4 = tens of minutes, bits 3-2-1-0 = units of minutes

byte hours_address = 0x02; 
byte hours;  // 7=0. 6 = 1 for 12 hr, 0 for 24 hr.
// bit 5: 12 hr mode = AM(0)/PM(1). 24 hr mode = upper tens of hrs
// bit 4 =  lower tens of hrs, bits 3-2-1-0 = units of hours (0-9)

byte day_week_address = 0x03; 
byte day_week = 0; // range 01-07

byte date_month_address = 0x04;
byte date_month = 0; // range 01-31

byte month_address = 0x05;
byte month = 0; // range 01-12

byte year_address = 0x06;
int year = 0; // upper byte 0-9, lower byte 0-9

byte square_address = 0x07;
byte sqwe = 0;  // square wave enable
// Out-0-0-Sqwe-0-0-RS1-RS0
// Out, Sqwe = 0/0 - Square wave output = 0
// Out, Sqwe = 1/0 - Square wave output = 1
// Out, Sqwe = 0/1 or 1/1 - Square wave output per RS1/RS0
// RS1/RS0 = 00 = 1 Hz
// RS1/RSo = 01 = 4 KHz
// RS1/RS0 = 10 = 8 KHz
// RS1/RS0 = 11 = 32 KHz

byte RTC_ram_address = 0x08; //range = 08-63, 0x08-0x3F

int RTC_address = 0x68; // 1101 000 

byte incomingCommand = 0;
byte RTC_write_command = 0;
byte RTC_read_command = 0;
byte RTC_ram_command = 0;

// use F0xx, F1xx,F2xx, F3xx, F4xx, F5xx, F6xx, F7xx
// to send one register write commands

byte incomingRegister = 0;
byte RTC_register = 0;
byte incomingData1 = 0;
byte incomingData2 = 0;
byte new_data = 0;
byte outgoingData = 0;
int delay_time = 100;

unsigned long currentMillis = 0;
unsigned long previousMillis = 0;
unsigned long duration = 5000;

void setup() {
  Wire.begin(); // no address, we are master
  Serial.begin (57600);  
  Serial.flush();
  currentMillis = millis();  
}

void loop() {
// this part lets you enter the date, time, year into the RTC from Serial Monitor

  if (Serial.available() >3){
    incomingCommand = Serial.read();
    incomingRegister = Serial.read();
    incomingData1 = Serial.read();
    incomingData1 = incomingData1 - 0x30; // convert ASCII to HEX
    incomingData2 = Serial.read();
    incomingData2 = incomingData2 - 0x30;  // convert ASCII to HEX
    new_data = (incomingData1 << 4) + incomingData2;  // put the Upper/Lower nibbles together
    Serial.print ("command ");
    Serial.println (incomingCommand);
    Serial.print ("register ");
    Serial.println(incomingRegister);
    Serial.print ("data1 ");
    Serial.println (incomingData1, HEX);
    Serial.print ("data2 ");
    Serial.println (incomingData2, HEX);
    Serial.print ("combined data ");    
    Serial.println (new_data, HEX);
    
  }
  // *******************************************
//  RTC_write_command = incomingCommand & 0xF0;  // mask off high byte
//  if (RTC_write_command == 0xF0){  // check for Write command
if ((incomingCommand == 'F') | (incomingCommand == 'f')){
  incomingCommand = 0;  // reset for next pass
//    RTC_register = incomingCommand & 0x0F;  // mask off low btye
//    incomingCommand = 0;
//    new_data = incomingData;
    Serial.println (" Sending a command ");
//    switch (RTC_register){
switch (incomingRegister){
  case '0': // write seconds
        Serial.println ("Seconds ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(seconds_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
      delay (delay_time);
      break;
    case '1': // write minutes
    Serial.println ("Minutes ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(minutes_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
      delay (delay_time);
      break;
    case '2': // write hours
        Serial.println ("Hours ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(hours_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
    case '3': // write day
        Serial.println ("Day ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(day_week_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
    case '4': // write date of month
        Serial.println ("Day of Month ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(date_month_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
    case '5': // write month
        Serial.println ("Month ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(month_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
    case '6': // write year
        Serial.println ("Year ");
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(year_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
    case '7': // write square wave
        Serial.println ("Square Wave ");
    Serial.println (RTC_register, HEX);
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(square_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
    case '8': // write RAM
        Serial.print ("RAM ");
    Serial.println (RTC_register, HEX);
      Wire.beginTransmission(RTC_address); // select device
      Wire.send(RTC_ram_address);          // queue the register
      Wire.send(new_data);                  // queue data
      Wire.endTransmission();            // send it
     delay (delay_time);
      break;
      // all others,do nothing
      Serial.println ("Invalid command ");
    }  // end Switch
  } // end if command == 'F'
  // ************************************

  currentMillis = millis();
  if ( (currentMillis - previousMillis) >= duration){
    previousMillis = currentMillis;  
    // Reset the register pointer  
    Wire.beginTransmission(RTC_address);  
    Wire.send(0x00);  
    Wire.endTransmission();   

    Wire.requestFrom(RTC_address,8 );  
    seconds = Wire.receive();  
    minutes = Wire.receive();  
    hours = Wire.receive();  
    day_week = Wire.receive();  
    date_month = Wire.receive();  
    month = Wire.receive();  
    year = Wire.receive();  
    sqwe = Wire.receive();

    // Seconds 
    // bit 7 = Clock Halt, Enabled = 0, Halt = 1
    // bits 6-5-3 = tens of seconds 0-6,  bits 3-2-1-0 = units of seconds, 0-9 

    // Hours
    // 7=0. 6 = 1 for 12 hr, 0 for 24 hr.
    // bit 5: 12 hr mode = AM(0)/PM(1). 24 hr mode = upper tens of hrs
    // bit 4 =  lower tens of hrs, bits 3-2-1-0 = units of hours (0-9)

    Serial.print ("Hrs " );
    Serial.print (hours, HEX);
    Serial.print (" Mins ");
    Serial.print (minutes, HEX);
    Serial.print (" Secs ");
    Serial.print (seconds, HEX);
    Serial.print (" Day ");
    Serial.print (day_week, HEX);
    Serial.print (" Date ");
    Serial.print (date_month, HEX);
    Serial.print (" Month ");
    Serial.print (month, HEX);
    Serial.print (" Year 20");
    Serial.print (year, HEX);
    Serial.print (" Square Wave ");
    Serial.println (sqwe, HEX);

  }
}