I can tell only so much from pictures, so I offer a few opinions.
I see no evidence that the lock was ever a flintlock. The square or clipped tail on the lock plate is a characteristic of a late Henry Leman lock of the percussion period. There is an extra hole in the lock plate near the nose. This appears to be the stud hole for the original main spring that was on the lock. I believe the lock has a modern replacement mainspring which required drilling a new hole in a slightly different location.
There are two lock bolt holes in the lock plate bolster suggesting this lock has been on another gun or older stock.
Henry Leman normally marked the rifles his company made on the lock and on the barrel. Since you didn't find any marks on barrel, I suspect that someone other than Leman made this gun or another possibility is that this is a relatively modern parts gun assembled from antique and possibly modern parts.
The "unknown holes drilled into the top of the barrel" suggest that a peep sight or even a scope had been mounted on it. This was sometimes done in the middle of the 20th century when interest in muzzleloaders and black powder shooting was beginning a revival, but before reproduction guns were widely available. People often shot antique guns or fabricated shoot-able guns from antique parts.
The original rear sight dovetails appear to have been filled. One with iron or steel and another with a copper colored metal.
It's hard to tell, but it is possible that the stock is modern. I notice the color of the wood in the lock mortise is about the same as the fresh wood exposed in the broken wrist. I would be interested in seeing pictures of the wood under the butt plate and in the barrel channel.
You didn't mention if the barrel is rifled or smoothbore. The octagon to round barrel isn't common on rifles of this period. Does it look like an antique or modern barrel?
I would also like to see pictures of the bottom of the barrel showing the front half of the bottom flat. Looks like there might be some other extraneous holes there that might tell us more about its history.
The patch box only has two screws holding it on and these are in the finial. The two side plates appear to have nails holding them on. This style of patch box was used by a number of different gun makers, including Henry Leman, but most used screws to hold the side plate on as shown in the montage below.
It's hard to tell from the pictures alone whether this is an antique patch box or a modern reproduction.
Anyway, just some observations.
