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The engine sure is not designed for some of this stuff (I'd have to add lots, including letting Rewind cross levels, to properly accomodate this kind of design), but your efforts are commendable. I couldn't figure out some of the later puzzles, but there are some very clever tricks ard dungeon design here.

I had to keep things the way they were in the main game because each level ultimately has to be self-contained enough to beat no matter what state you reach it in, even if you use Restart, or else you could get stuck (and for the purposes of time trials, too). And it's hard to force a split when the girls don't start out split; making Brooke Berserk away is the easiest way, but that doesn't show up until late. A few levels do it, but it's risky to have it span multiple levels if there's a chance of getting on the wrong sides. So yeah, that's an advantage of custom dungeons.