so it turns out doing relative file paths for the symlink worked a treat, but i was still having issues with config.txt
I managed to track it down though. Mounting the boot partition, changing the config, then unmounting wasn't actually working!! if i re-mounted again straight away, it would be back to the original files.

I found a fix though, you have to mount the loop device with a sync flag, this stops it caching the changes and makes it work as expected :)

thanks again for your help @mitu :)

ok so further testing. If i use adafruit retrogame, i see Joy2key appear in Top at about 20% cpu, then after a few seconds it disappears.

Using my own code, Joy2key does the same 20% ish cpu for a few seconds, then it will sit at about 4% cup for as long as im playing a game. it actually remains even when i close the emulator (start + select)

pi@retropie:~ $ udevadm info /dev/input/event0 P: /devices/virtual/input/input0/event0 N: input/event0 E: DEVNAME=/dev/input/event0 E: DEVPATH=/devices/virtual/input/input0/event0 E: ID_INPUT=1 E: ID_INPUT_JOYSTICK=1 E: ID_INPUT_KEY=1 E: ID_SERIAL=noserial E: MAJOR=13 E: MINOR=64 E: SUBSYSTEM=input E: TAGS=:seat:uaccess: E: USEC_INITIALIZED=16949167 pi@retropie:~ $ dmesg | grep -i input [ 16.015469] input: TinyPi-Pro as /devices/virtual/input/input0