This sounds very interesting and clearly you have given it a lot of thought already. There are a few things I am wondering though.
Are you planning to follow what is shown in Episodes 1-6 as being set in stone of are you happy to do a Lucas and ignore a few bits here and there if it makes it easier to fit your stories?
I'd like to have it based on the Adywan revisited Saga. So, e.g. if he really is to kill off Lando at the end we'll don't have him in sequels. The choice, maybe, is between having the sequels to adapt both to the GL and Revisited versions (Lando is not shown but we don't know where he really is) or just the Revisited (and have someone says something like "poor Lando, killed during the death star II assault!")
But basically, I'd preferred not to contraddict the movies.
But, what are the "few bits" you'd like to ignore?
By your circular theory of Episodes 1-3 being the dark side of the yin/yang, and then Episodes 4-6 being the light side of the circle, then your Episodes 7-9 would focus on that dark spot and moving back into the dark side. If I have understood this correctly doesn't that suggest either your Episode 9 will end on a bad note (like Episode 3) with a bad side victory, or you would have to fit a full cycle (like from Episodes 1-6) into your 3 part story?
From what we can see in the movies, the time for a cycle is variable. The Jedi in TPM are without Sith from a millennium. then, in less than 40 years we have a full cycle. Now we can both have a complete cycle in 3 movies of just half. We don't have limits, IMHO.
Or just have the characters (Luke) understand this and "pass the knowledge" so that when the time of a new chosen will arrive, the jedi will have better understanding of what's happening.
we could just see the black spot rise.
Anyway, afterward I'll post some other material about that.
This makes me wonder because either you could choose to ignore the ending of RotJ and imagine the Emperor escaped alive and then he can be your black spot bad guy, presumably ending the trilogy with his defeat. Or if you treat the films as absolute then you would need a new enemy, a little like what happened in the Heir to the Empire books.
making the emperor alive is like undertone the same prophecy. And it's very similar to dark empire.
I'm to post something on that afterwars but, yes, this is one of the most difficult part. To have an enemy and not made him simple repetition of what we alredy saw.