Yup, they'll swap over without any problems.

I added the Savage rails and sissybar to my S40 last year.

The only thing that will be missing is a small grommet at the back of the fender. On the S40 rails, there is a little "nub" that sticks into the hole. The grommet just sort of holds it in place I think, might prevent vibrating too?

I outlined my swap and the differences between the S40 rails to the S40 sissybar rails, to the Savage sissybar rails... It's over on my BikePics page:

http://bikepics.com/members/simontuffguy/07boulevards40/

If you look at the shot of the fender without the rails, you can see the little black grommet that is in the hole.