The brake will go all the way down and does not hit the lower wind fairing.
The mounting is exactly like the original and the difference is just in the lever itself.
My concern was not that the end of the pedal would not go down past the end of the running board, it looks like it would without any issue. My thought was that your foot would come down flat on the running board and there would still be more pedal available. The only way in my mind, if this is the case, would be to hit the pedal pad with your heel to get the remaining travel of the pedal in an emergency.
I'm sure that in good working order, the pedal stops way above the board, but when the turds hit the rotisserie unit and you need that pinch more, it's not available.
There is probably nothing to worry about and I'm just being paranoid about my thoughts.
I did basically the same thing on my old '76 FLH as the pedal was almost straight up. I cut my pedal and "V'd" it and re-welded it to a more comfortable position. I did check to make sure it bottomed in the cylinder before bottoming out on the running board.
The new pedal all chromed up does look VERY nice and would be a great addition to any of our bikes.