As for other game play elements, in very long scenarios my granaries would occasionally all stop working at the same time. They were not labor-starved, they were not cut off from the city in any way, and all would shut down at once. I asked the forum about this , the docks, and a rumor that the Cleopatra add-on allows monuments to be sped up, and the only answers I received for the granary problem seem to have missed my statements that they are not cut off from labor. The only solution I discovered was to destroy them all and rebuild them, which means losing whatever food they had in them at the time. As for the other questions, no one really has a solution for the dock problem, and it seems that Cleopatra allows pyramids to be sped up by blessings from some gods.
Gods are important in Pharaoh.
You must please them with temples, shrines, and festivals or they will hurt your city. If you keep them very pleased, however, they can really help your city, almost to the point of cheating. For example, the cat-headed goddess Bast will throw festivals for other gods and fill your bazaars and homes with goods. Ptah will fill storage yards with goods, which can be extremely profitable. If you don't also keep Pharaoh happy, he will eventually send his army against you and destroy your city.