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.
The right way to fix this is to have a local engineer size a LVL (laminated veneer lumber) beam for you (solid wood lumber won't meet modern standards for a span that long). It'll likely be taller than your current beam. You'll need to temporarily support all the rafters with a framed wall on each side, using double top plates. Keep them a few feet away from the beam to allow room to work. Remove the existing beam, the posts supporting it, and all metal hangers.
The new beam will likely be 2" thicker than the current one--LVL beams are often 1-3/4" thick per member, and they're usually doubled in cases like this. This will require trimming of the rafters on one or both sides.
Slide the new beam into place and support it a few feet from each end with temporary posts. Fit new posts using adequate lumber. Double 2x4s may be enough, but ask the engineer. Install the same hangers if they're appropriate, or use new ones.
Alternatively, you may be able to install your new beam directly below the existing beam. Of course, this dramatically reduces headroom. I expect a new beam to be sized at around 12" high.
Best Answer
Gussets wouldn't replace a ridge beam (which is different from a ridge board). You'd need a truss design with collar or rafter ties.
If you don't have a ridge beam (which actually carries the load from the upper half of the rafters), you need rafter ties, which run across from wall to wall. Gussets don't provide the sort of bracing that rafter ties would.