...Crayauchtin's alive? I forgot he even existed.
As far as combining the TSL and AGDI timelines together, I'd say keep the Father from KQ2+ in the story, but only refer to him by his real name (Morgeilen) and treat him like a lesser servant of the Black Cloaks, sort of like an enforcer, and not the Big Bad. And finally, have Graham actually kill him in combat instead of just letting him get away on a crappy cliffhanger that ultimately goes completely unresolved. That way, Shadrack retains his status as the Bigger Bad throughout the series up until TSL.
I'd love to write my own stories set in the KQ universe, but I'm waiting until TSL episode 5 is released so that I have the entire picture in my head. I wouldn't want to release one story after another just making up sh*t as I go, not knowing how the whole thing would actually end. Think of all the foreshadowing one could do with the knowledge of TSL's entire storyline. Hell, you could probably incorporate MoE into there with enough work and not have it stick out like a sore thumb. The whole plot would have to be rewritten, of course, and Connor would actually have to be likable, but I'm sure it's possible.
In fact, I say you could even make Cedric likable by changing him around a bit. And not, you know, get himself in trouble repeatedly. I swear, first he gets nommed by a wolf, then he gets beat up by harpies, then he gets stuck under boat debris upon crash-landing onto Mordack's island, then he gets blasted by Mordack...and through it all:
"Graham, help me!"
Give me a reason to, you little tw@t.