One of the best ways to clean rust from the bore is to use a bronze brush where the twisted wire is threaded through the shank and not crimped, the crimped type will pull off. Then get a
"Big 45 Frontier Metal Cleaner" pad, unravel and cut about a 12" length of strand from the pad, then twist it around the brush bristles and use like you normally would use the brush. The pad is made of an alloy that will not scratch the bluing like steel wool will, but will remove rust. I have used the pads to remove rust on many different types of firearms and tools for over 30 years and it works, and will not scratch like steel wool. I would not use it on browned metal, but for muzzle loading bores it is perfect.
To clean/scrub the face of the breech plug, I cut a dozen or so 2" lengths of strand from the pad and thread them through the eye of a shotgun cleaning tip which you can get an adapter to fit a standard cleaning rod. Center the strands where you have an equal length on either side of the eye, then fold the ends forward and wrap with several wraps of dental floss, essentially making a scrubbing mop in order to get at the face of the plug.
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This link to the company's website provides all the details on how to use the pad, and instructions on how to use it wrapped around a cleaning brush for removing rust, lead, and fouling from the bore.
"Big 45 Frontier Metal Cleaner Pad"