It's been a while since I last re-read the books, but wasn't the whole stagnation and death thing part of Paul's attempt to avoid the jihad in the earlier parts of the first book? By the end, his experiences had altered his perspective after becoming trapped by his own vision. Also a bit fuzzy on the details, but I recall a conversation between old blind preacher Paul and Leto where Paul flat out says he saw the path Leto has chosen, could have initiated it himself but was repulsed by the prospect.
It's just my interpretation but I always equated this difference to Paul being raised as a person before awakening, whereas Leto and Ghanima were abominations and thus had a wider perspective on what is personally tolerable. The only real human bond they had was for each other, which was again why Leto went through with it: to spare Ghanima from the agony.
The way I picture it, CoD would end with a coda that depicts what is described in the opening excerpt from GEoD, with Odrade opening and exploring one of Leto's storehouses and discovering his journals. A scene that will be later revisited in full.
HoD should start with Duncan's (latest) birth, though one could do an artful credit sequence depicting the broad strokes of the intervening history. Either more literal like the openings of 'Watchmen' & 'Wolverine: Origins' or something more abstract, perhaps with pictographs or similar symbolic rendering played to music.