MK is a pain in the ass to setup.
If I remember right the buttons are assigned like this.
123
45
1 High Punch
2 Block
3 High Kick
4 Low punch
5 low kick
so if you have this
123
456
and have it setup for SF you need to do is go into your mame menu and scroll down to button 5 in the menu and press enter, escape (or whatever buttons you have set to confirm and clear). This will clear the button mapping. Then press enter again and push what button you want to be low kick.
That should do it I think.