The fairing stay has a different part number. So investigate whether you may add this to you swapping to the S2 fairing. I know only the prefix on the part numbers are different but it's worth checking out.
S1 is 5vx-28356-00-00
S2 is 4s8-28356-00-00
Edit: Looking at the pictures of the stay brackets, they are definitely different so if you go the S2 route you'll need the S2 stay and it's $138 US at Ronayers.com Ron Ayers Motorsports