Dave, as for how Brother Dain can be connected to Alistair... You mentioned that he has split most of his adult life between Flamekeep and his ancestral holdings near the Thrane/Karrnath border. Would anything in or near his ancestral holdings have been potential targets during the war? I ask because I see two possible scenarios for how Dain met him...
1) One of the times that Dain temporarily dropped his research to come to aid in the defence of a church or monastery under attack, it could have turned out that the property either belonged to Alistair or was located near some of his property. If Alistair himself was there at the time, a lone monk coming to give aid likely would have been brought to his attention. If he was not there at the time, a report mentioning Dain's aid still might have been given to him.
Either way, Alistair might have decided that he wanted to meet this monk and offer his thanks. And since he has ancestral holdings near the border and carries rank, he would be a prime interview candidate for Dain's research. I imagine that someone with Alistair's background and rank would be intrigued by a monk who is attempting to objectively document border disputes, yet who drops everything to come to the defence of one particular side of the War. Dain is a proud citizen of Thrane and a tithing member of the Church (something else that would probably pique Alistair's interest). As such, it is quite a contrast for him to state that he is being objective in his research. I am sure that some portion of this would appeal to Alistair's eccentric nature.
2) Dain may have become aware of one of Alistair's periodic visits to his ancestral holdings. Given the man's rank and background, Dain would become quite interested in getting his view of the border disputes for his research. He would petition for an audience, and presumably it would be granted. From there, this would proceed pretty much the same as the above, just without the battle at the beginning.
Once they got to know one another, Alistair would likely come to view Brother Dain as someone who can be counted on. He is a loyal Thranish citizen, and he pays a hefty tithe to the Church. From their discussions on his research, it would become apparent that Dain can take care of himself and get done what needs to be done. And of course, I am certain that Alistair would have also done his own background check, and would know Dain's complete history.
Either of the above would help take care of how Dain knows Alistair. But I am at a bit of a loss as to how Dain would know the rest of the characters. Due to his research, Dain has spent nearly his entire life around the Thrane/Karrnath border. He would, however, come to Flamekeep is summoned there. Particularly if the summons came from Alistair.
So aside from the possibility of Dain and Drue crossing paths while visiting the same church near the border, the most likely scenario for Dain to know the other characters is to have worked together with them on some task for Alistair previously, either all at once or different characters at different times. Can Dave give more detail as to what Alistair has had us do in the past? Or should we just take it at value that we have all worked together before for Alistair and that we all know and trust one another by now?