1: "To think the it would split in a direction like this." What would split if not time/alternate realities/dimensions? "You've progressed too far; I need to find another point." Another point where he hasn't progressed too far is the only way you can read that sentence, as in he has to either go back in time to where you haven't progressed, or, something that's a bit more likely, travel to a different dimension where this hasn't happened, anchor both of your existences together, and kill that one. Deus also being a quite clear reference to "Deus ex Machina" it stands to reason that there's more to him than meets the eye.
2: Absolutely, but all of this makes sense if he doesn't truly believe she's dead in the first place, or he doesn't want to be forced to explain what he saw when he scanned "her" corpse to HERO or be mindscanned forcibly. All of these presuppositions are obviously just me handwaving something which could mean something in the story, or more likely it's just WW either a: writing themselves into a corner or b: slipped their mind.
3: A plothole is a very specific kind of story error, this is just characters acting in stupid ways, which isn't a plothole in itself. Regardless, his transforming of other people isn't easy, and him transforming alpha breaker wasn't done while he was currently exploding into pieces, same with Johan and the trap, he could take his time and make sure none of the power went out of wack and suddenly there's a 10 feet tumorous head on her corpse. There's more information on the minutiae of how his transforming power works if you go the Snow White route iirc. You have to take into account that her head is currently in pieces and he's using his concentration to keep the pieces from flying off, in addition to being a brain, orders of magnitude more complex than whatever he's done previous.
A known bug, will be fixed in the public release.