Greetings Vand1,
It is no secret that I am totally opposed to using the hot water and soap cleaning method.
Your rifle has a powder chamber a 1/4 inch or smaller in diameter, so you are correct in using the flush tube.
Do yourself a good turn and buy a product name Black-Solve. Dixie Gun Works sells it you can not find it locally.
Use Black-Solve to clean the barrel and flush through the breech and drum as usual. No need to remove the nipple if you do not want to. A piece of 1/8 " soft rubber tubing will fit quite nicely on the nipple.
Put about 2 " of Black-Solve in the barrel. Use a snug fitting patch on the ramrod and use a plunging motion. Flush through the nipple and tubing. Do this twice, then clean the bore with Black-Solve until the bore is clean, and dry with one or two dry, clean patches.
Wrap a dry cleaning patch around a 22 caliber bronze/brass cleaning brush and use that to dry out the trapped moisture in the powder chamber.
Now comes the important part. With the tubing still on the nipple, squirt WD-40 down the bore to run out the moisture residue in the breech and drum threads.
This is probably the source of your rust.
Dry the powder chamber and bore and coat the bore with RIG Grease. Forget the Bore Butter except as a patch lube.
If you are not sure about this cleaning method, ask Davy about his Pedersoli Flintlock.
Best regards and good shooting,
John L. Hinnant
If you are not an NRA Member, why not? I am carrying your load.