The S-40 and the S-50 share a near identical rear profile. Same shock mounts, same turn signal location.
Any saddlebags listed to fit the S-50 will fit the S-40 as well.
If they don't list the S-50, look at the VL800/Volusia. Same thing.
Parts are interchangeable.
Or find a saddle shop/leather shop and have a set custom made. I had mine done at Lutz's Leather in Elwood City, Pa (
www.lutzsleather.com ) $280.00 and worth every penny.