Williams Cleaner rounds, which were included 1 round in a 10 round pack of .58 minies, fell out of use because there were doubts of its effectiveness of cleaning the barrel. They were essentially standard lead rounds with a zinc washer at the base.With properly sized ammunition, a Soldier could expect to fire 60 rounds between cleanings. As the war progressed the diameter of the bullets got smaller to aid in loading.
No minie cartridges, north or south, American or English manufacture, had paper rammed with the bullet. The minie didn't work that way.
You can't load a .54 ball into a .58 barrel. You can, but the bullet would have extremely load velocity and no accuracy and be pretty useless. Heck even a properly size .58 ball is not effective in the shallow grooves of the .58 Springfield/Enfield.
Both the north and south continuously manufactured black powder throughout the war. The north had the DuPont family, and black powder was one area that the South had great success in making a great deal and of high quality.
I am not going to pretend I know as much about muzzle loaders as you. As to the Author's contention that the Williams Cleaners were curtailed because the Union was largely switching to multiple round weapons I thought sounded a little crazy. I thought it was basically the Calvary which were issued these weapons and single shot muzzle loaders were used right into 1865.
As far as loading problems with Enfields, I do believe the author is correct and provides, page 261, "...in Dec '62 the Ordinance Bureau issued a circular , warning arsenals to limit the size of Enfield Ammo......in June of 1863, Gorgas's Top Assistant Major JW Mallet, recieved a complaint from a general officer in Lee's Army....probably Rodes, that Enfields clogged too frequently most likley from gunpowder and grease from cartridge cases...."
Page 262. "I have been informed by a letter from a General Officer in the ANV, Mallet alerted Gorgas, "that the men repeatedly sought to obtain Miss. Rifle ammo. (cal. 54) for thier Enfields and Rifled Muskets (Cal 577 & 58) - such was the fear of jamming of bullets in the bore derived by previous experience." citation #16.