Your campaign sounds great so far. I think you made the right moves having reoccurring organizations after a desired artifact, family motivations, as well as an enemy-turned-uncertain-ally. I also love the alterations to the
KotS and TL, and I'm a sucker for time travel. The players sound happy and you appear to have had a good time thus far, which is really what's most important.
At this point I wouldn't feel stuck over the possibilities you've given yourself. The reoccurring organizations and Skather help unify them all, as well as the promise of a BBEG (even if you don't exactly know who that is yet). I'm in a similar boat with my campaign, as the major villains have changed and changed again over the course of 8 levels.
I think you should continue doing what you've been doing, running adventures featuring the BoV, EC and Zenobal until they find natural conclusions, or until they provide a juicy means to reveal more of Tiamat and/or the Rajah.
You should avoid being too hasty in ending any branch. I think if you keep following all your factions, the players will unwittingly help in developing the conclusions for each. Besides I feel like Paragon and Epic levels have a lot of room to fill, and if you start narrowing things too quickly you could run the risk of being repetitive or predictable.
As it stands, you have a lot of mystery and potential in the game, so much that even you haven't figured it all out yet. I think that's the best place to be. It's obvious you can string a story, so trust that and continue to take it forward. Take advantage of what you know the players like, Stormreach for instance, and go from there. Xen'drik has plenty to work with. Perhaps you could integrate some Revenge of the Giants for later Paragon, or borrow from the other adventures you see promise in. It seems to have worked for you thus far.
I don't think I quite answered your question, but good luck!