"What does it matter where the threads of the breech plug are or how long they need to be?"
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If the plug is short of the rifling, there is a gap at the back of the barrel, and in front of the breechplug face, where crud builds, and corrodes the barrel.
That is a very dangerous situation over a number of years. Think where that barrel will rupture and how close it is to your face and hands.
The guy who built my .50 caliber rifle screwed this up, leaving a gap about 1/8" wide in front of the plug.
Thankfully, I decided to convert the rifle from percussion to Flint about a year later, and the gunmaker who did that work removed the breechplug, and discovered the mess! The corrosion was there, but not deep enough to be a danger, yet.
I had some idea that the barrel was not right, because no matter how much soaking and pumping, and cleaning and drying the barrel after shooting it, A dry patch run down to the breechplug face would always come back with a "ring " of black powder "stain" on the patch, as if there still was crud in the "corners" of the bore that I was not getting. Of course, I used a scraper to try to get this, too, but that didn't work, either. When we put a light down the bore, the plug looked bright and clean, as did the barrel and grooves. So, where was that crud coming from?
We ordered a new Breechplug, and its threaded portion was actually shorter than the threads on my older one! That is when I found out that there is no consistency in plug length in the industry. And that is when a phone call to the barrel maker- to see if he had a plug the correct length-- alerted me to the fact that extra length was routinely left at the back of the barrel, with the expectation that the gunbuilder would file it down to get the correct fit.
IT IS TRADITIONAL that barrel makers stamp their marks on the flat that represents the side of the run-out, so that the run-out is going down. Then, the builder can correct the problem with a higher front sight!
Today, most barrel run-out is either very small- much better boring equipment-- or non-existent, as the barrelstock is first bored and rifled, and then the flats are cut with the barrel held on centers in the bore, eliminating any run-out that existed at the end of the boring process.Its not uncommon for barrels made this way to have NO stamp or mark on a flat, other than the company's name, and it doesn't matter which flat is placed down. Out of tradition, most builders continue to orient the barrel, so the manufacturer's name is on the bottom flat of the gun.
When barrels were forged, the flats were forged first, and then filed on the barrel, BEFORE the bore was drilled. If the drill bit hit anything in the steel blank, the bit could turn and would then drill off-center, leaving "run-out". Run out is simply the difference from "square " of the bore to the outside diameter of the barrel. If the bore is drilled straight, it will be parallel and " Square to the outside diameter and dimensions of the barrel.