f its " Brown" , its " flash rust", caused by using water that is too hot. Hot water is not a substitute for Soap and water, and time. Let the soap eat the dirt loose. Too many young ( to the sport) shooters are in too much hurry to get the cleaning chore done when they get home. I was that way, too. I also thought using really hot water- just short of burning my hands, was necessary.
I now have taken the advice of a friend, and use tepid water- skin temperature or air temperature-- when cleaning the guns. The Flash rust is no longer a problem.
There will be graphite that works into the pores, and leaves you with gray streaks from the grooves long after the lands are shiney, and clean. Part of this comes from the fact that only rarely are the grooves actually as polished smooth like the lands. Part of this is due to the depth of the grooves, and the difficulty getting a patch down into the corners. Unless you are fortunate enough to be shooting a round bottom groove barrel, the only way I have found to get down into the corners is to use a patch over a Bore Brush when cleaning.
I also use alcohol or acetone to get at the graphite, as it seems to work better at getting into the pores than does mere soap and water. Acetone is nasty stuff, so do this outdoors, and keep your nose upwind of the barrel. Wear rubber gloves to protect your hands, if you have them. Alcohol is less hazardous, but you don't want to spill it on your hands, either. Both evaporate rather quickly.
If rust has eaten even tiny holes into the grooves of the barrel, residue, and graphite buildup in those holes, or pores, is going to be a continuous problem. The graphite is just a form of carbon, but its what it might have in the pores with it that is a concern. Alone, it would not be a concern, as carbon is rather neutral.( Think Diamond)
So, use cool water, at least for your rinse, to cool the barrel so it doesn't immediately rust when pull a cleaning patch out of it and expose it to still moist air. Then pour some alcohol down the barrel and slosh it back and forth and shake the barrel up and down to let the alcohol get at the graphite. Pour out the dirty contents, and then use a patch on a bore brush to get down into the corners and get the graphite out of the corners. A dozen or more strokes with the bore bursh, changing the patch as it gets dirty, will usually get the graphite out of the corners of the grooves. Then a few more clean patches down the barrel, followed by a patch with oil or lube, in front of a cleaning jag, should set the barrel up for storage.
Most of all, I have found I can't hurry this process very much, or I still have gray streaks on my oil patches when they come out.
Oh, I early on found that using my ramrod for cleaning was a PITA! Its just not long enough, even with the jag, or bore brush in place, to allow much of a purchase with my wide hands. So, I highly recommend you invest in a range rod and use it for all cleaning chores.My ramrods are the first articles on my gun that are removed and cleaned. Then they are set aside while I work on the barrel, and lock. the last thing I clean is the stock, after I lube the outside of the barrel with wonderlube. Wipe fingerprints and acids, and residue off the stock and barrel first, of course, but I found that wonderlube does a very good job of preserving my brown finish on the barrel and other parts. The stock gets wiped down with a clean cloth, then gets a coat of wax before storing.
Oh, a last comment on your post. You mention using Peroxide/alcohol mixes to clean. Peroxide is a very harsh oxidizing agent, and eats iron and steel like a SNACK! It will leave black or dark gray streaks on your patches untiL *ell freezes over, or until you stop using it. Use Peroxide ONLY when having to really go after built up crud- the kind you find in used guns because the prior owner didn't clean it. Peroxide works wonderfully, for getting under crud, breaking it up, so you can pore it out with the waste water.
But, Don't use peroxide in the final stages of cleaning. Just clean water, and then clean alcohol.
I use to use peroxide to get that the crud down in the corners of the grooves, but It became next to impossible to tell from looking at the patches whether I was getting crud, or the dark residue from the corrosion caused by the peroxide. A wiser shooter told me to stop using the peroxide, and the "problem" ceased.
If you go up to the member resources here, and scroll down to Stumpy's mixes, you will find he does not use peroxide at all in any of his lubes, or cleaning compounds. I was using a formula I got out of Muzzle Blasts years ago that called for a small amount of Hydrogen Peroxide mixed with Water Soluable oil, detergent, and water for both a lube, and a cleaner. The peroxide is no longer a component.
I suggest you give these ideas a try, and see if they don't help you out. :thumbsup: