Yup, all those things you mentioned were loose ends in the original BG, though I sort of felt that the special secret area in the Temple Sewers was kind of the climax for the Illithid-related stories.
As far as plotline connections, I would reach all the way back, beyond the origins of Mind Flayers in D&D. With a little online research, you will find that Gary Gygax created them after seeing the cover art of a book called "The Burrowers Beneath", by Brian Lumley. Lumley, in turn, was inspired by the writings of H.P. Lovecraft such as "the Haunter in the Dark". I think the older BG series had sort of captured the Lovecraftian theme somewhat, that there are entities in the universe to whom mankind is insignificant. The best we can expect from such entities is indifference, and in the worst cases of dealing with such creatures, our perceptions of reality are shattered and we devolve into madness and chaos. Lovecraft was a genius at capturing the horror of the unknown, and I hope Larian takes advantage of this wonderful legacy.
