the 120kb is likely the lessest size. You may can use compiler optimization to reduce code size. You can change the I2C eeprom on the board, it should have a IC socket or you may use the 4Mbit SPI flash which is also on the dvk board.
The small eeprom is enough to tell the FX3 a customer specific VID and PID and to save some variables, but you may not really get such a huge I2C eeprom to save and load the application file. What you can also do with the I2C eeprom you can put on a bootloader for FX3, the bootloader is way lesser than 32KB in release version.
hope this helped you out...
I see, thank you. I am going to change it to 24LC1024.