I'm considering the slanted layout like in that link. If I do a straight SF style do you have your Button A on the second row like this?

No, I have D there.
A is the first in the top row.
Not trying to recreate the original layout.
I like this for the Namco fighters as well instead of the original square.
My thumb and first finger are left kick and left punch.
My middle finger and ring finger are right punch and right kick.
The buttons are easier to reach and it makes sense in my mind.
That's how I would do MK3.
For some reason I don't play MK3 as much as the first two.