I’ve now read the article by Ugo Zanetti, “Abu-l Makarim et Abu Salih”, Bulletin de la societe d’archeologie copte 34 (1995), pp.85-138, which seems pretty thorough on all the confusing information around. Rather than leave my questions hanging, I thought I would answer it myself for the benefit of those reading and not as obsessed as myself!
There are two, and only two manuscripts; Paris arabe 307, and Munich ar. 2570. The latter once belonged to Girgis Filutaus (who was Rector of the Coptic Cathedral in Cairo), but arrived in Europe a couple of decades ago, in a very bad state.
Evetts published the Paris ms in 1898, with an English translation. This is missing the introduction, but ends with a colophon.
Fr. Samuel published the Munich ms (then still in Egypt), and used a modern copy of the Paris ms. in the Coptic Museum. His edition was in 4 parts, part 4 being indexes etc. Part 1 and 3 were from the Munich ms; part 2 from the Paris ms, where he improves somewhat on Evetts edition.
Zanetti analysed the two mss codicologically and found that they were originally a single manuscript, which was dismembered centuries ago, before the Paris ms was bought in Egypt during the 17th century. The Munich ms. is the start of the ms. and should be followed by the Paris ms. So the correct order of the parts in Samuel should be part 1, part 3, and then part 2. (Samuel was misled by the hand of the scribe, which changes part way through the ms and then changes back, and by the fact that he didn’t have access to more than photographs of the Paris ms.)
An English translation exists of part 1 (only) of Samuel’s edition. This is
Bishop Samuel, “Abu al Makarem”. Trans<lated> by Mina al-Shamaa`. Rev. by Mrs. Elizabeth (= “History of the Churches and Monasteries in Lower Egypt in the 13th century”), Cairo, Inst. des. Etudes Coptes (Anba Ruwais), 1992.
It also includes some maps and an index. A copy exists in the US Library of Congress.
So no translation exists of part 3 (i.e. the middle part of the work).