Of all of those, only Miho is really problematic in the storyline they're tackling from the comics. Bob plays a bit more of a role, but he wasn't a major character in the first. Manute is barely in it (and as you said, no choice but to recast there) and I don't remember Shellie in that story at all.
It sucks that they've had to recast anyone (other than Dwight) but I can't imagine it making that big of an impact on the film. Or at least not anymore than recasting Rachel after Batman Begins.