James,
Sorry I haven't gotten back to you on the barrel gunk, been a little preoccupied. I would first run a few wet patches using some strong cleaner like Barnes or possibly even Sweets mixed with a little Kroil. This will let you know right away if it is copper or not. If so it will generally take it out in short order and a good oiling afterwords will leave it non the worse for it. If it isn't copper, then you might try using the Flitz or JB paste on a patch and a .410 jag and see if that don't get it.
In all the years of owning the SS Rugers the only actual rust I have seen on them has been on the main spring of my 41 which got submerged. Even that was mainly only superficial and with some Scotch Brite and Kroil it cleaned right up. I haven't been overly tender with any of mine in that we hunt no matter what the weather. Sometimes they are wet for several days on end depending on where we were hunting, and how well things could get cleaned up. Either my 41 or my 44 generally rides in the holster around the handle bars of my Polaris for easy access if we encounter a pack of hogs. With the weather and dust, they have survived much longer than some which would cost much more and have accounted for many pounds of pork.
Good luck with yours and I would wager that what your seeing is not actually rust but is probably fouling as has been mentioned.