I could not get the gap between the stock floor boards and te bottom edge of the inner panel to line up so I spliced another small piece of sheet metal in its place.

As for getting the indents to line up, this sounds line you are splicing in to some of the existing panel's remains. You might have to replace the entire panel if this will be a problem to you. I plan to cover my inner panels with carpet or speaker panels so I was not too concerned about the alignment.

The major pain of replacing the entire panel is the weatherstripping channel needs to be removed. I drilled out the spot welds holding it in and then cut the channel where the patch panel needs to go. I then reattached with spot welds in the holes I had already drilled.

The front cowl panels are some of the more difficult on an AD in my opinion as the patch panels are not ever quite a direct fit.

Good luck