i fixed the first to by editing the the mupen64plus.cfg file and the InputAutoCfg.ini file in the /opt/retropie/configs/n64.
just when you edit the inputautocfg.ini file to remap buttons it does it for all games running that profile. just look in the file for the name of the controller your using and remap the keys the same as the retroroach.cfg
the last im still looking for has to do with changing the mupen64plus.cfg where it says
# Joystick event string for stopping the emulator
Joy Mapping Stop = “”
i like to know if you find what to put there.