These are all my own personal interpretations of the (poorly written) rules, and have no official standing, but I thought I'd lend out another opinion at least.
Ikkok-Ikki regoup: the image example set on page 19 shows 3 different regrouping areas, but the two on the left should be just one, for the sea zone connects both. Right?
The rules state (11.3) that groupings are determined by lines of communication. In 5.2 it states that lines of communication are blocked by enemy units and also if any spaces along the trace are not controlled by the unit's faction. Further, in 2.44 it says that sea areas are like waypoints, and then in 2.46 it says that waypoints are never controlled by a Clan, they are considered friendly to both Factions throughout the game.
So I think you're probably right. Unless there were an enemy unit in the seas space, the grouping should be considered in communication and just one grouping.
During our game, Ukita leader defects to Oda along with his accompanying soldiers, and then goes and takes his former Ukita home castle to Oda control. What happens? Does the Ukita clan fall, which would say all ukita units go to Oda's pool and Oda takes control of each and every Ukita space?
That sounds correct to me.
Also, is the fall of clan immediately during a game turn disregarding any phase, as soon as its conditions are fulfilled?
I think the clan falls immediately when the conditions are met.