As promised, here is a summer query of my own. Please send me yours, and I’ll happily post them.
Along with Christophe Grellard, Zenon Kaluza, and Aurélien Robert, I am working on a new edition of Nicholas of Autrecourt’s Tractatus (aka the Exigit Ordo). Because the work is known to survive in only one manuscript, we feel some temptation to preserve the manuscript’s orthography. But we hesitate, because it is not clear that this has significant value to scholars, and clearly there are attendant inconveniences. Hence, we solicit your advice.
In medias PHIL 
Dear Bob,
I’m all in favour of normalizing the orthography as long as nothing substantial hangs on it. It is less distracting and makes the reading much easier. You’ll be normalizing the punctuation anyway, I take it.
Best regards, Claude
Claude Panaccio Chaire de recherche du Canada en Théorie de la connaissance Département de philosophie Université du Québec à Montréal C.P. 8888 Succursale Centre-ville Montréal, Qc, CANADA, H3C 3P8 Tél. (bur.): 514-987-3000, poste 1916
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I recommend the advice of Paul Tombeur, ‘De polygraphia’ in A. Maieru, Grafia e interpunzione del latino nel medioevo, in Lessico intelletuale europeo, XLI (Rome 1987) pp. 69-101
I would normalize the spelling…it’s such a pity the Leonine edition has recently begun to preserve the archaic manuscript spellings…recently I puzzled over “es” (you are) in Aquinas’s Commentary on Physics for quite some time before realizing it meant “aes” (bronze)! I had to go back to the Greek to be sure. Medieval shorthand was meant to facilitate copying manuscripts, something that is no longer a concern. I think it’s best to just footnote or otherwise indicate where there really is an ambiguity, e.g. when, say, “rosae” could conceivably be either dative or genitive. In my experience, this is only rarely the case.