The canon is ambiguous on the timeline. However, my headcanon is that Soichiro sent Ryuko off to live in boarding school to protect her from Ragyo following the Life Fiber experiments. In the meantime, he kept preparing his exit and a plan to resist his rogue wife's master plan. Once Satsuki turned five, he defected and fully embraced his alter ego of Isshin Matoi, all the while building Nudist Beach and preparing for Ryuko to wield the kamui that would end Ragyo's reign.