I want to use a USB controller or change the keys for the directional cause my keyboard arrows are acting strange so i cant use right + up or right + down

You can use a xbox 360 controller with if it has a USB output yeah. Not sure about other types of controllers though. And I'm pretty sure you can change some the controls in the game to move with other keys then the arrow keys. Not sure if they keep between save files though.

I tried to change the keys, but the changes does not affect other save files

https://joytokey.net/en/ might help