Is that a floor board/toe board combination? If so, that is where your sheet metal skills will need to come in.
Your new inner cowl looks to me to be correctly bent at the bottom.
I would remove a section of the old floor, and the old inner cowl, then screw the inner cowl panel in place with small self-tapping screws.
After that you will need to message the floor/toeboard to match the new inner cowl and install it
