Cay, I know you know this, but when I clean my flinters, I take the lock off, put a toothpick in the vent and pour water or your preferred cleaner down the barrel...I pour that out and most of the residue goes with it...I then run 2-3 patches down the barrel and put the toothpick back in and pour water down the barrel again and pour out...This time I dry the barrel, shoot some WD-40 down the barrel, dry and then oil...I then clean the lock and I'm done...
Frankly, my Knight Disc takes me longer to clean than my flintlocks...
On the barrel...I have to admit I cheated...When I made mine, I bedded the barrel, each year I seal the edge of the barrel with my patch lube which is mainly bees wax...
The funny thing is, who cares if a little rust forms under the barrel, it's not going to hurt anything in our lifetime...