By the way, it's something that most people forget when they do these things, or make evil fan-fics/parodies, but Littlefoot and friends are in no danger from the meteorite. The K-T event is centuries away, as the end of the first film clearly states, "And they all grew up together in the valley, generation upon generation, each passing on to the next, the tale of their ancestor's journey to the valley, long ago".
With this in mind, we can actually assume that the GOF remained in the valley, grew up and had kids, and their story became a popular legend (Makes you wonder if 2-13 became folk stories, hence the moral in each of them).
As for the bizarre events that have befallen everyone (Meteor showers, famine, snow, etc), the films also state that the lands are changing. I guess it's the end of an old Cretaceous epoch and the beginning of a new one, so new plants, animals and stuff like that are arriving (Instantly, as cartoon logic shows us).
(Also, a good thing about gaps in fossil records, is that you can use them as loopholes. For instance, they say that Apatosaurs and Stegosaurs would not have lived in the Cretaceous, but that's because no fossils have been found. So, you can twist the facts to somehow, but not exactly accurately, explain things in LBT)
Actually, I'm going to continue this from the last post; The way I'd end the series, would be the same as above, but in addition, we see one of the GOF's kids telling the story of the first movie, maybe even quoting it while the GOF's ghosts watch. You could even jump forwards years and years, seeing the story getting passed down, and even end the film with the same ending words of the first. Then, as they say that, pan the camera up to the stars, and see several shining stars standing out, representing the GOF (The Big Dipper, for instance. Seven stars, that includes the GOF, Chomper and Ruby).