bleach and a scrub brush should take care of most of it. you could paint over it after with some anti-mold/mildew paint.
The bigger problem I can see is wind-washing. Basically wind come up hard through your soffit and blows your insulation around and then over time, it drops down your soffit vent and clogs your soffit which inhibits proper air flow and keeps your roof decking from drying properly when you do have problems like that. its usually not a problem if your trusses have energy heels on them, but most houses that are few years old now just have the regular trusses.
It might be smart to clean out your soffit and extend your soffit vents an additional 4 feet. I tape them up at the seams and over the staples into the roof decking. And definitely get the roof fixed. Most likely a sloppy flashing job around the vent penetration in the roof next to the mold When the7 pull the shingles up, I would ask them to use window flashing around the external vent. you begin by placing the tape over the bottom (part of the vent closest to the eve) first, then a piece overlapping on each side of the vent, and finally at the top (the part closest to the ridge). half of the tape will be on the external vent and th other half should form a water tight seal on the roof decking. Caulk around it, relay the shingles, and then apply roofing caulk.