The Menuet differences are substantial enough to suggest Keller represents a revision. I am not knowledgeable about the manuscript history, but is it possible Bach revised the suites at some point after Anna made her copy?
As far as my knowledge goes, there is no revision by Bach. The "Cothen Years" are known as "crazy in work tempo" that he left so many pieces incomplete because of lack of time.
what's the last note of the second group, D or E? As I'd read it (not being familiar with any of these hands but from these short excerpts) I'd say with Anna it's clearly a D, while with Keller, it's an E again (same as the second note of the group)?
You are right but there is no way to know.
That's my impression too but I don't have the booklet to confirm. I'd also be interested if anyone has Wispelwey's III's booklet to see if he is influenced by the Anna Magdalena phrasing there, as I suspect.
In general, it says for the III, because of the mystery, he sat down with John Butt of Glasgow University and Laurence Dreyfus of Oxford University and 'found plausible and playable solutions to a number of fascinating performance issues' of Anna's
I'm with Jeffrey: the minuet differences look more like a revision than a transcription error.
It might not be that simple as there are other details. For instance, including Kellner and Anna, the total of manuscripts from that century is four and lately they dated Kellner to 1726 and Anna to 1727. The pitch difference on the last picture is only on Anna's which chronologically makes the last note: E (kellner-bach alive)- natural B (anna- bach alive), E (Westphal-bach dead), E(Traeg item by an anonymous copier 1799-bach dead).
Anyway, when there is no composer-autographed score from 300 years ago you can speculate on everything. We even love to speculate on originals...so...I just wanted to give the gist of difficulties of authenticity.