Morphy
You don't need a tar file to update you can use the img.gz file too.
Never knew that, thanks! Thought this was for new installations only 
Anyway I've updated and it works out of the box now thanks! I have some more issues now though
I can't exit from any game and no hotkeys work now so I'm guessing these need setting up in RA.
The ES controller config has nothting to to with the RA setup and is only used for controlling the ES frontend. It also depends in which mode you've connected the gamepad so if it works in Xinput or Dinput mode. Both feature a different number of buttons. Your controller isn't included in SDL2 upstream gamecontrollerdb sdl_gamecontrollerdb.h so it won't be detected out of the box. Or in other words... you saved on the wrong things 
Ah ok I thought the controls were configured in ES for all libretro emu's. Strange how you have to configure ALL the buttons just for a menu system... And yes, I was surprised it worked so well in RP to be honest!
If your controls are weird in RA you have a faulty config file. Also check you controls per emulator. You can for example enable anlogue to digital for games that don't support sticks but this cause problems in other games that have mapped controls on the sticks.
Where do I check the controls per emulator? I looked at User 1 binds in RA and mine is set to Retropad w/Analog. User 1 Analog to digital is set to None. Not sure why N64 analog is messed up 
I'm not adding back the quit menu because it's not functional since it's made for RetroPie and makes no sense since LE has it's own shutdown function.
Ah ok. I just thought on the rpi when it comes to shutting down it's quicker to shut down from ES then having to go back into kodi.