Thanks a lot

Adding an options screen would probably be a bit annoying, as the code is very closely based on the original arcade Z80 structure (with whatever overhead that might result in) - I did do something similar when testing the game, on the "push only 1player button" screen, where I replaced the text with two options (starting level and starting screen/board index) that could be changed by pressing up/down or left/right, coincidentally saved in the saveram similar to what you suggest.
As it is, it's a little hard to add any more code to the game without moving into bank switching, as I used as much space I could for the sound data - the PRG rom is completely packed

If you want to remap what buttons are checked for left, right, up and down in the game, I think it would be easier to just identify the areas where these directions are checked, as opposed to the controller reading routing - however it's worth noting that in Donkey Kong left/right isn't just used for controlling Mario, but the barrel AI and the jump detection (when jumping "over" an item) also check for the direction pushed.