So we got to the rank 3 locations so the smelly guy spawned and I put the abomination in the lair. His nemesis ability is to engage a player. Does this pull him from the lair or do you get to ignore that particular ability untill he spawns on his own at the end of the adventure?

I think this one was answered on BGG. If the Nemesis is rolled the effect applies, and he comes out early.