What I may do is make transparencies so each main character has their own timeline and the transparency overlays allow me to see where they intersect so I can make sure they interact at the right times. It will also (hopefully) limit the number of primary characters.
I'm trying to keep the storylines focused on only a few people, even though there may be a "cast of thousands". I want to be vested in just a handful of characters, and I find I want to follow the stories of many more.
Right now, I have Ptahmose, and his new mentor Siamun, and waiting in the wings is his soon-to-be wife (name not yet chosen but she'll be an important character for a while and then make sporadic appearances after they are married - she may assume greater importance, not sure yet). Connected to him and making sporadic appearances are his parents, his siblings, his favorite teacher, and at least one of his childhood friends.
There's Neferkhamun and his twin brother Neferptah. Neferkhamun runs the sepat, and Neferptah runs the main city. There are their families, wives, children, other siblings and their families.
Living in Neferkhamun's household would be the upper staff - not servants, as they have a high enough status to have servants of their own, private apartments in Neferkhamun's mansion. These would be managers, in corporate structure, they'd be upper management, division heads. These are currently lesser characters, background people who come to the fore only if they are needed, but hovering back there. If it were being filmed, you'd see them in the distance, like fellow cubicle employees. Ptahmose was among these people - as a scribe, he held near noble rank, and his position came with property that would support him, his servants, and the family he would have.
And then there are the servants, the people who did the work while the others managed, intrigued, and planned. Kitchen staff, house servants, gardeners, stablehands, nursery helpers, laundresses, food servers, messengers, and so on. Some would be slaves, but slaves in ancient Egypt held a different status than slaves elsewhere. Often slaves held a higher status than the villagers and farmers, the peasants who could be conscripted to build canals, temples, pyramids, granaries, and other public buildings.
I don't have any solid hold on the servants and saves in Neferkhamun's household yet. I do have a slave that has had some interactions with Ptahmose and may end up assigned to help care for Ptahmose's household within Neferkhamun's household. And there's a gardener and a gate guard that are fleshing themselves out because of interactions with Ptahmose, Siamun, and Nefekhamun.
Then there are the friends of Neferkhamun and Neferptah, and their rivals.
The sepat is not an isolated place, and it has a varied alliance with neighboring sepats. Also, because they are on the Nile, they have accessibility to the other sepats, so there would be the rulers of these sepats.