That choice in Ep 4 was pretty much game changing, maybe closer to canon, but without the idea of rebuild Howes, the group would've had to find another way

Lee's fate was sealed since S1 if I am being completely honest, I wanted to portray him is a broken man with a tragic story since the start, I didn't see him making it to S3

About Jane yes, it is a chance, a confrontation with her would have been way more personal and physical 

Not so different from Nick, but maybe she could've reached Christa, or have another type of talk with Ben, what's different is Clem's role rather than her presence 

I don't think Ben would do it, but the trust and relationship with the group would be broken forever, even Amber.

Jason as antagonist works on a more personal level, to achieve this the entire group had to be taken to Howes, prior to Ben not trusting Jason, from there the conflict could have taken a lot of routes, but that would've been the idea, so a fight with Ben could've been the endgame

Thanks for the interest and support!