I've been thinking a bit about the background of this Thunderscorn based army. For whatever reason, from a narrative perspective, I really like Ghur, the realm of beasts. Part of what made me finally take the plunge on Dragon Ogors was the fact that it gave me an excuse to take monsters in may army. I really liked the book Bladestorm, which followed Thostos Bladestorm, a Lord Celestant of the Celestial Vindicators, as he leads a Warrior Chamber into Ghur to take a Chaos fort with a realmgate in order to complete some mission that I frankly forget (at that point it got a bit less interesting for me). It was a pretty typical Realmgate Wars story, but there were a lot of things I really liked. There was a tribe of humans awed by the Stormcast and thought they were angels sent to help them (they didn't). It humanized the Stormcast as well as showed their very non-human aspects. There were some epic battles (of course) with the Stormcast fighting a fort full of Khorne warriors and deamons. It also introduced the Ironjaws as they attack the fort. My Stormcast army are Celestial Vindicators based in Ghur. I put them in the "present" 50-100 years after those events. They are part of the Vanguard chamber left behind in Ghur to guard that area.
The new official fluff for the Thunderscorn is great. For those that haven't read it, they use to live in Azyr until kicked out by Sigmar prior to closing the realmgates. They really resent that and have been trying to get back there for a thousand years (or something like that).
My idea for the thunderscorn, is that the Shaggoth was whiling away the centuries in the mountains of Ghur, as they are wont to do, contemplating ways to get back to Azyr and take revenge on Sigmar. From those mountains he saw the entrance of the Stormcast into the realm and watched the battles at the fort and the reactivation of the realmgate. He recognized the Stormcast as children of Sigmar and therefore understood that the way to Azyr was now open. From there he started the long process of planning and mustering the other Thunderscorn of the realm as well as other allied beasts that he could bend to his will. This puts him in the same "present" as my Stormcast. His plan is to come down out of the mountain, take the fort and realmgate and make his way to Azyr, fighting anyone in his way (of course) creating his own mini realmgate wars.