I am so far behind on this thread, I'll never get to read it all! So I apologise if this has already been covered. Re the garrote - wasn't JB's hair found to be tied into the knot? if so, it wasn't from something else and repurposed, nor was it made earlier. If her hair was caught in the knot, it means the cord was tied around her neck, not tied then put over her head. This also means that it couldn't have been pulled tight once tied, as her hair would have been yanked out.
A few years ago, there was some discussion here about this, and the theory was floated that maybe the garrote was tied around her neck to explain marks caused either by a hand or by something else.
Also, I'm wondering whether some of the staging actually happened during John's missing time. Run with me here: BR hits JB, wakes/gets PR (if she didn't actually go to bed). She also panics, writes the note, stages JB to look like a sexual assault - hands overhead etc. JR wakes up in the morning, realises the note is hinky but doesn't know what has happened. Insists on the 911 call. Goes looking for JB during the time is is 'missing', finds her, can't have her found the dramatic way PR has staged, dresses her in the Bloomies panties (has to use them as they're the only thing available in the basement, and he can't go running upstairs to her bedroom for a pair that fit), wraps her in the blanket and moves her so that he can 'find' her later. There's still several problems with this scenario, but I do think the idea of JR changing the staging during his missing time may have legs.