how long does it take until the eggs of a hen run their course from one roo so that I am certain all of her eggs are fertilized from the next roo she is breed to?
It's common to allow three weeks after removing one rooster, before starting to collect eggs from the next rooster.
If you just remove the rooster, you will typically get fertile eggs for the next week. The second and third week you might get a few fertile eggs--not enough for a good hatch rate, but enough to mess up a breeding program with "oops" chicks. (Having the new rooster present may mean that his sperm outcompete the older sperm to fertilize the eggs, but it's not a guaranteed thing.)
But sometimes you can set it up so you know which rooster fathered which chick, just by examining the chicks.
A few specific examples:
With your Easter Eggers and Ayam Cemani: if the hens are brown and black, they will produce black chicks when bred to the Ayam Cemani. If the Easter Egger rooster is also brown and black (not all black), or if he is brown and white, those same hens will produce not-black chicks when bred to him. So you could just sort the chicks for "black" and "not-black." (Might be able to sort at hatch, might have to wait some weeks for them to get feathers--depends on the genetic details of the color patterns involved.) Most white-and-black patterns would work equally well, but there are a few that won't.
For testing Ayam Cemani hens: of course pure Ayam Cemani will be black. If you cross with a splash rooster (two copies of the blue gene), then all chicks from that rooster will be blue instead of black. Or cross with a white-laced-red rooster, and you'll get white chicks (because of the Dominant White gene turning the black to white.) A Barred Rock or Dominique rooster should pass barring to all his chicks, which would distinguish them from pure black Ayam Cemani chicks. (Does not work with a Black Sexlink rooster, because he has only one copy of the barring gene, so only half his chicks will be barred.)
A bird with a crest on the head, or feathered legs, will typically pass those to its chicks, so those can also be used as markers of which rooster was the father.