I would suggest the following:
The Mother's metal polish or Meguiers metal polish or Flitz metal polish. All are excellent cleaners and will yield the result your after.
Second...I would use a cordless drill and remove good many of the screws than are in the rub rail. I remove about six or so, this is far easier than cleaning out the phillip heads stainless screws. Then if you have an old wool pad and an obital polisher, at a low speed polish the stainless rub rail. If you don't have an obital then a micro fiber is your best choice. Your working toward seeing a lot of black it the rag or wool pad. Pressure/fiction is what works the best. You'll see.
If you are serious about the shine...after you buff, use lemon juice and wipe over the rub rail. A little goes a long way. It cleans out that black stuff from the pours of the metal.
Cleaning the rub rail is time consuming but if your a shine person its will worth the effort.
Also using Acetone on the plastic backing of the rubrail or any place on the fiberglass, will remove any marks and will NOT hurt the plastic or the fiberglass. Acetone is one of the ingriedents of the gelcoat.
Post the after pictures. I'll clean mine and post a few pic's with a "how to"