Also I did not see where you were using wood restore as a final treatment, we have not done a cedar shake roofs yet but the wood we have done, we finished with wood restore and that gave it the light golden appearance.
The UV and mold damages on the wood will be coton white. This needs some time to weather off if the roof was pretty badly infested. On smaller areas we reccomend using a deck brush to remove the fuzz. On roofs it just takes a little time for the UV damaged wood to wear off.
Most likely it is not the black mold/fungus but tanin. Take a photo when dry. A lot of it will go grey and blend in. They don't always get the golden hue. Here is some photos before, after and one year later.
The black stains may be from treating the shakes in the past. In Texas they use to treat the shakes with deisle fuel regularly believe it or not. I dont think those black streaks are organic though.
Looks Good. The black definitely is Tanin. I believe you need a higher PH soap like Terra Wash. Spray mix on, let it dwell 10 - 15 minutes. Rinse with your booster pump with a garden hose and a zero degree tip, moving quickly across each black section, like your are trying to rinse a stubborn piece of dirt.. That should loosen the tanin, Then reapply your solution and it should even out the coloring. As it dries the coloring will even out the grey over a few months.
It is a type of a color fast fungus. It is dead. Just leave it. The rain will wash it off as the roots decompose. We see it on occasion on asphalt roofs and concrete. It it is new it will come off, if it has been there a while it will just take time. Do not use too strong of a mix.
Remember that these roofs didnt get this way overnight and often times the solution doesnt have overnight results either. Important to set the expectation.
The mustard colored algae you are seeing is what we now call California Golden Algae. It is colorfast and does not bleach out. It however as Tim mentioned dies and rinses off after several rains.
I used to have a roommate named Rob Baxter when I lived in Norfolk, VA about 15 years back. :0)
Back on subject, I haven't worked on any cedar shake roofs yet, but I've seen that orange stuff a couple of times. I was helping Mark Fermoyle on a roof the first time and we had some orange fungus or lichen like that. Mark was using a 4% mix and it didn't alter the color of the growth at all. I saw it again while cleaning my brothers roof and sprayed it with about a 3 1/2 SH/CH augmented mix and went back over it a couple of passes. The other lichen and moss around it was a nice cotton white, but the orange really doesn't change color much, if any at all. When I came back later it had decomposed and washed off the roof along with everything else. It's just something to keep in the back of your head when setting customer expectations.