Does rukia ever realize that Kaen Shiba is related to ichigo in canon?
I don't think she ever put the pieces together, only that Ichigo looks like Kaien.
When will Ishin regain his power?
He's got, I think, a year or so left? If I remember correctly, the Quest starts a year before canon right? Because Isshin's power comes back when Grand Fisher returns for round two, and gets insta-ganked by Captain Dad.
So there are at least three captain strength soul reapers in Karakura Town
Two for the moment sadly, Isshin isn't available.
Throw in the two pure quincies, multiple full bringers, and the visored and you have a living death trap for hollows.
And that's why Karakura Town is a Juureichi. Also, the Fullbringers haven't awoken to their true nature yet.
We could start by awakening thier latent shinigami Powers, and unlock ishin
That's a Bad Idea(tm). Not the least of which being that it would be either Karin or Yuzu in Aizen's sights as a Plan B if the process succeeds, and if not, Ichigo just killed one or both of his sisters and due in to the Gotei 13 to stand trial for interfering in the human world and attempting to create Shinigami. As for Isshin, his issue is resolved in another year or so, so no need.
then contact Urahara's candy shop to befriend them as friends of the family
Urahara is already in contact with Isshin.
Finding a way to befriend the Ishidas would also be a good idea, Ishin is already friends with Uryus father.
...that might be difficult considering Uryuu would just want to kill Ichigo as a Shinigami. Isshin and Ryuuken aren't exactly friends, but it's close enough.
At the very least point out what Ichigo's mother and father are to Uryu
That requires IC knowledge Ichigo does not have at the moment.
protecting them might make himess hell bent on hating soul reapers
Considering that the Soul Reapers more or less orchestrated the death of closest family member at the time, I seriously doubt that Uryuu's hate-boner for Shinigami will eventually fade in this quest like it did in canon because Ichigo is no longer around him to bridge that gap.
Wait, if the twins were born after Ichigo could they also have hollow or fullbringer Powers?
IIRC the hollow that was within Masaki was transferred to Ichigo when he was born. I think that was when Masaki and Isshin began the slow as fuck process of regaining their powers.