I am only just starting this adventure so I may post more at a later date.
But this adventure carried no Affiliation Award side bar, and my PCs still need some assistance with building up their scores, so I went ahead and created the following.
Each of the following criterions grants an affiliation score modifier of +1.
Church of the Whirling Fury, The Dawn Council, Emerald Crest, and The Scarlet Brotherhood:
Destroy the Crimson Fleet pirate base and terminate Cold Captain Wyther with extreme prejudice
Rescue the pirate captain Harliss Javell and recruit her into the Emerald Crest.
Recover the Athrinoord Stone found in location H4 and donate it to a Seeker Chapterhouse.
Recover a serpent symbol and donate it to the Witchwardens in Sasserine for study.
Capture the fiendish eye of the deep and return it to Sasserine alive for the arena, or slay the yuan-ti anathema and bring its corpse back to Sasserine as a trophy. Accomplishing both tasks nets PCs with this affiliation a +2 to their score.