jhave_21:
do you think I could still use the arduino IDE.
If you are using an Atmega2560 microprocessor with an Arduino bootloader you can use the Arduino IDE. Indeed you can use the IDE even if there is no bootloader if you can connect to it to program it using ICSP.
As @-dev has said the IDE uses a boards file that assumes a particular mapping between the physical I/O pins on the chip and the I/O pins on the Arduino Mega board. If you want to change that relationship you would need to write a new file with the your relationships.
If all you want to do is omit several pins then as long as your program does not try to use the missing pins there should be no need to change anything.
...R