According to the introductory discussion by the editors, the Assisi manuscript 137, A in the app. crit., is only trustworthy to around distinction seven of book III. It also is trustworthy for all of book I up through d. 2 of book II; I don't know about IV (though it is probably discussed in the lengthy prolegomena to the entire edition in vol. 1 which I haven't waded through yet). A professor of mine who taught manuscript editing and worked on the Scotus de anima questions was highly critical of the vatican editors use of this manuscript, which purports to be a copy of the Liber scoti. This latter ms. was Scotus's autograph, probably kept at Oxford until it was burned by the prots in 1535 or 1550. It is imporant as it contains lots of marginalia designating the order of paragraphs and additions, deletions and other authorial notes. Its text serves as the base text of the edition, save where the editors find it untrustworthy (bks 2 and 3). According to my professor, though the comments is preserves are precious, and the scribe probably did have some access to the autograph, he only wrote in Scotus's comments; the text itself is from somewhere else, and is inferior to some of the other manuscripts in the tradition. I'm still trying to sort all this out and don't have strong opinions either way.
That's all for now, I hope you all run out and by vol. X. I know you want to.