How to use the untraced pins for ATmega2560?

Hello.
On the original Arduino from ATmega2560 chip not all port pins are traced (for me interested this ports: 29, 47-48 - they are comfortable to trace on my board).
Is it possible (and how) to use them in the Arduino IDE?

Yes, it is possible to use any pin in the Arduino IDE. This is a matter of SW. If the pin is not configured in the Arduino SW, you can modify the pins_arduino.h for the mega variant and add it to the configuration. For the AVR tools you need not to do anything.
The second thing is the HW modification. It is a problem. A long time ago, I made modification on my Mega 2560 R3 board due to pin 29 (TOSC1) usage. I connected Atmega's pin 29 to the N.C. pin on Arduino's power header by a wire. Header pin is marked for 'future use'. It should work for you also but what about the rest 2 pins. You have to solve the HW to add the connector or what. It is on your imagination.