Whoa.
As I understand it:
CHANGE 1: Lama Su says Qui Gonn ordered the clones. Obi Wan reacts (although he doesn't have to repeat the name if you don't want, Trooperman. His lines where he actually repeats the name are less than essential-- but if they work they will help the audience confirm they heard this bomb-shell correctly).
CHANGE 2: Dukoo says that Qui Gonn HAD LEARNED the truth of the Sith when he invites Obi Wan to join him (this can be done with a small edit). He does not, however, mention the clones. No need to add that and tip Dukoo's hand.
CHANGE 3: Dukoo flies to Sidious and reveals that the war has begun. Dialogue to be written will allow Dukoo to also clarify one of the following (we need to pick one):
a) Qui Gonn actually ordered the clones, but Dukoo and Sidious somehow tricked him into it.
OR
b) it was actually Dukoo who ordered the clones and used Qui Gonn's name to do it.
So we need to pick a direction and then write the brief, but believable expositional dialogue that gets us there in the end.
I think I vote that Qui Gonn actually ordered the clones, but I don't know exactly how that gets clarified in the end. What does Dukoo say? The jist should be either: "Good thing Qui Gonn ordered those clones?" or "my apprentice fell for our trick, Qui Gonn's clones are operational!"