Figured it out. For anybody using keyboard or ipac. It is the /opt/retropie/configs/n64/InputAutoCfg.ini file. If you dont have it plug in a controller and go through the controller config from emulationstation start menu and it will create one. Then change controls for the keyboard in that file. I found the keys from http://www.vizzed.com/boards/thread.php?id=79869