Any moisture issues related to the standing water incident would have manifested itself long before now. Whatever the current issue is, it's unrelated to the previous issue. In that time, it is possible a new leak developed. It's also possible the dark areas are related to interior humidity and unrelated to the roof. In cold weather, the ceiling surface under rafters is measurably cooler than the nearby portion under insulation alone. This can cause condensation only under the rafters. As you know, condensation can lead to mold.
Can you tell if the darkening is due to actual mold? The damp surface can attract dirt that darkens the area even though no mold is growing. Even though the dirt can stain, attempting to clean an area with plain soap and water would yield a very different result than if mold is actively growing.
If mold is actively growing, it is time to consult with a mold professional. They will determine the cause, mitigate the mold, and suggest how to prevent it from happening again. If you want to investigate further before going that route, the only reliable way to determine if the rafters are getting wet is direct inspection.
Cut a small inspection hole where you think it's the worst. If it's wet up there, a lot more ceiling is coming off, so don't bother patching the hole. The roof is leaking. It needs to be repaired and all wet drywall and insulation needs to be replaced. If it's all dry, breathe a sigh of relief. The need to patch the hole is much less than it could have been. Be sure to adequately seal the damaged vapor barrier.
If the rafters are dry, the only thing you can do to reduce condensation on the ceiling is reduce the overall humidity of the house. First try selective ventilation and lifestyle adjustments. Consider bumping the thermostat up a bit. If that's not enough, look into continuous ventilation through an air to air heat exchanger.
A far as replacing stringers, that cannot be done with comp roofing unless a full cold roof is installed. It is normal practice for concealed structural spaces filled with insulation to not be ventilated. It sounds like the roofers followed conventional building practice.
I called an engineer and paid for his evaluation of the wall. It's not load bearing. Realized that I left out some basics about the house.
This house is built on a raised foundation with cripple walls attaching the floor joists to the foundation. The metal post is attached to the fireplace foundation (which is independent of the houses foundation). There is no foundation (just 3 feet of empty air) underneath the wall I want to remove. The header is just oddly sized.
The header does not connect to the beam.
From a sheer wall perspective he was not too concerned, given that the total amount of wall I want to remove is pretty minimal compared to the rest of the house.
Best Answer
In brick/masory homes the vertical slots are called weep holes.
Their purpose is to allow the rain water that soaks through the brick to come back out. From what I learned, about 10% of what gets on the brick passes through since the brick is porous. On the back side of the brick there is a drainage plane, or surface that has been traditionally tar paper nailed or stapled over the wood framing. The paper is lapped so the water as it collects goes over the laps and continues down where the through wall flashing turns it back out the wall through the weep holes.
7-28-2018 edit
I just re-read the question and seen I really did not answer the question at all. The horizontal gap is typically not there. as Lee Sam mentioned, counter flashing should be there, but I hope is still there deeper inside the recess.
For some reason the builder decided to set the brick on a steel lintel (beam of a sort) above the roof, instead of below the roof where this space would not be seen. If the through wall flashing allowed it, typical counterflashing could still be applied although there would be no backer for it. Backer would keep it in a vertical plane. As a mention counterflashing is used to cover the base flashing that is covering the tops of the last row of shingles.
This sketch is not the only way to do it, but it is the best way to do it, IMO. The problem is, the potential to damage the all important through wall flashing is quite possible (the black line behind and under the brick).
To simply fasten something on top of the shingles for the sake of holding something in place to hide the gap would also have a strong possibility of making leaks in your roof.