Once a player, or the AI, control X% of Japan (the exact limit is not set in stone yet - and it will be moddable) he can declare himself Shogun. To become recognized as Shogun he however needs to hold this position - not slipping under the X% - for a number of months/years (again not set yet).
During this time:
a) other clans may attack him (and they will perceive him as the bigger threat)
b) parts of his clan may break out and establish themselves as independent clans
c) a member of the same dynasty may try and usurp the clan leader title through a plot
d) you might lose the clan leader title in election when your character dies
That a clan reaches the position of claiming themselves Shogun but then crumbles due to any one or a combination of the reasons listed above is not unhistorical - it happen a number of time. See Nobunaga and Hideyoshi.
I hope that make things a little clearer
