Thank you kindly! All great advice!I had the same issue with my 1803 Harper's Ferry. Modern breech plugs are much longer than the originals. Preformed stocks are designed for the shorter breech plugs to get the fence on the lock to line up with end of the barrel. This means that the ideal spot in the pan for the touch hole will be behind the face of the breech plug. I asked several highly respected gun builders what to do. The consensus was to make a dimple in the breech plug where the touch hole hits the threads. The breech plug face needs to be counterbored to the depth of the touch hole and a notch has to be cut to the counter bore. I was concerned about the exposed threads being a path for rust to form in the breech plug. Similar notches are common from paths from the touch hole to the breech face. When the breech plug is well greased, the rusting is not really an issue. What is important is establishing a path from the pan to the powder charge. Most original firearms with the notched breeches have intact threads. With a good path from the pan to the powder charge, ignition is fast.
So, @Joemolf, complete the notch and enjoy the performance you are expecting.
Joe